Locus 9628

Sequence ID 3R_DroMel_CAF1
Location 25,434,429 – 25,434,578
Length 149
Max. P 0.967386
window15394 window15395

overview

Window 4

Location 25,434,429 – 25,434,542
Length 113
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 91.89
Mean single sequence MFE -35.35
Consensus MFE -31.50
Energy contribution -31.75
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -1.68
Structure conservation index 0.89
SVM decision value 0.70
SVM RNA-class probability 0.828064
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25434429 113 + 27905053
AUUAGGGGCUGCCUUCAAGGAUCUUUUGCCAAGGACUUUUUGAAAAAGAACUACAUACACGGCAUCGAAUUGCUGGGCACAGAAAGGACCGAGCUGUGCUUUUUGUGCCAAUA
....((..((...(((((((((((((....))))).))))))))..))..)).......(((((......)))))(((((((((((.((......)).))))))))))).... ( -36.20)
>DroSec_CAF1 117264 113 + 1
AUUAGGGGCUGCCUUCAAGGAUCUUUUGCCAAGGACUUUUUGCAAAAGAACUACAUACACGGCAUCGAGUUGCUGGGCACAGAGAGGACCGAGCUGUGCUUUCUGUGCCAGUA
...((((....))))...((.((((((((.(((....))).)))))))).))...(((.(((((......)))))(((((((((((.((......)).))))))))))).))) ( -39.60)
>DroSim_CAF1 119195 113 + 1
AUUAGGGGCUGCCUUCAAGGAUCUUUUGCCAAGGACUUUCUGCAAAAGAACUACAUACACGGCAUCGAGUUGCUGGGCACAGAGAGGACCGAGCUGUGCUUUCUGUGCCAAUA
...((((....))))...((.((((((((..(((....))))))))))).)).......(((((......)))))(((((((((((.((......)).))))))))))).... ( -39.20)
>DroYak_CAF1 127511 113 + 1
AUUAGGGGCUGCCUUCAAGGAUCUUUUGCCAGCGACUUUUUAAAAAAGAAUUACAUACACGGCAUCGAAUUGCUGGGCACCGAAAUGAGCGAACUCUGUUUUCUGUGCCAGUU
......(((..((.....)).......)))...((((......................(((((......)))))(((((.((((.(((....)))...)))).))))))))) ( -26.40)
>consensus
AUUAGGGGCUGCCUUCAAGGAUCUUUUGCCAAGGACUUUUUGAAAAAGAACUACAUACACGGCAUCGAAUUGCUGGGCACAGAAAGGACCGAGCUGUGCUUUCUGUGCCAAUA
...((((....))))...((.((((((((............)))))))).)).......(((((......)))))(((((((((((.((......)).))))))))))).... (-31.50 = -31.75 +   0.25)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 25,434,469 – 25,434,578
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 90.21
Mean single sequence MFE -27.38
Consensus MFE -25.66
Energy contribution -25.35
Covariance contribution -0.31
Combinations/Pair 1.17
Mean z-score -1.99
Structure conservation index 0.94
SVM decision value 1.61
SVM RNA-class probability 0.967386
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25434469 109 + 27905053
UGAAAAAGAACUACAUACACGGCAUCGAAUUGCUGGGCACAGAAAGGACCGAGCUGUGCUUUUUGUGCCAAUACAUACCUAAGAAGAUUGAAUUUGAAAUAAAUUAAAG
...................(((((......)))))(((((((((((.((......)).)))))))))))........................................ ( -25.70)
>DroSec_CAF1 117304 109 + 1
UGCAAAAGAACUACAUACACGGCAUCGAGUUGCUGGGCACAGAGAGGACCGAGCUGUGCUUUCUGUGCCAGUACAUACCUAAGAAGAUUGAAUUUGAAAUAAAUUAAAG
..((((.............(((((......)))))(((((((((((.((......)).))))))))))).......................))))............. ( -29.60)
>DroSim_CAF1 119235 109 + 1
UGCAAAAGAACUACAUACACGGCAUCGAGUUGCUGGGCACAGAGAGGACCGAGCUGUGCUUUCUGUGCCAAUACAUACCUAAGAAGAUUGAAUUUGAAAUAAAUUAAAG
..((((.............(((((......)))))(((((((((((.((......)).))))))))))).......................))))............. ( -29.60)
>DroYak_CAF1 127551 109 + 1
UAAAAAAGAAUUACAUACACGGCAUCGAAUUGCUGGGCACCGAAAUGAGCGAACUCUGUUUUCUGUGCCAGUUCAUACCUAGAAAGUUGGAAGUUGCAAUAAAUUAAAG
.......(((((.......(((((......)))))(((((.((((.(((....)))...)))).))))))))))...((.........))................... ( -24.60)
>consensus
UGAAAAAGAACUACAUACACGGCAUCGAAUUGCUGGGCACAGAAAGGACCGAGCUGUGCUUUCUGUGCCAAUACAUACCUAAGAAGAUUGAAUUUGAAAUAAAUUAAAG
...................(((((......)))))(((((((((((.((......)).)))))))))))........................................ (-25.66 = -25.35 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:40 2006