Locus 1270

Sequence ID 3R_DroMel_CAF1
Location 3,782,826 – 3,782,985
Length 159
Max. P 0.903385
window2074 window2075

overview

Window 4

Location 3,782,826 – 3,782,945
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.15
Mean single sequence MFE -42.02
Consensus MFE -35.10
Energy contribution -36.54
Covariance contribution 1.44
Combinations/Pair 1.03
Mean z-score -1.68
Structure conservation index 0.84
SVM decision value 1.03
SVM RNA-class probability 0.903385
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3782826 119 + 27905053
UAUGACUAAUUCCGGAGUCGGGCAGCGCCAGCGUGGGCAGCAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGGGCGACUAGGA-AAUUUGCAACAAAGUUGCCAUGGCCGGCUGGAAA
.........((((((((((((((.(((((......))).)).(((((......)).))))))))))).(((...(((((((..(.-.........)..)))))))..)))...)))))). ( -42.80)
>DroSec_CAF1 12263 119 + 1
UAUGACUAAUUCCGGAGUCGGGCAGCGCCAGUGUGGGCAGCAGGCCAAACUAAUGAGCCGUCCAACUUGUUUUGGGCGACUAGGA-AAUUUGCAACAAAGUUGCCUUGGCCGGCUGGAAA
.........((((((.(((((((((((((......))).((((((((......)).)))((((((......))))))........-....)))......)))))).))))...)))))). ( -42.20)
>DroSim_CAF1 15982 119 + 1
UAUGACUAAUUCCGGAGUCGGGCAGCGCCAGUGUGGGCAGCAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGGGCGACUAGGA-AAUUUGCAACAAAGUUGCCUUGGCCGGCUGGAAA
.........((((((((((((((.(((((......))).)).(((((......)).))))))))))).(((..((((((((..(.-.........)..)))))))).)))...)))))). ( -43.40)
>DroEre_CAF1 2614 120 + 1
CUUGACUAAAUCCGGAGUCGGGCAGCGCCAGUGUGGGCAGCAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGGGGGAUUAGGAAAACUUGCAACAAAGUUGCCAUGGCCAGCAAGAAA
((((.((...(((((((((((((.(((((......))).)).(((((......)).))))))))))))....))))((....((..(((((......))))).))....))))))))... ( -39.50)
>DroYak_CAF1 15982 119 + 1
CAUGACUAAUUCCGGAGUCGGGCAGCGCCAGUGUGGGCAGCAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGG-GGACUGGAAAAAUGUGCAACAAAGUUGCCAUGGCCAGCAAGAAA
.....((((..(..(((((((((.(((((......))).)).(((((......)).)))))))))))))..))))-.(.((((....(((.(((((...))))))))..)))))...... ( -42.20)
>consensus
UAUGACUAAUUCCGGAGUCGGGCAGCGCCAGUGUGGGCAGCAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGGGCGACUAGGA_AAUUUGCAACAAAGUUGCCAUGGCCGGCUGGAAA
.........((((((.(((((((((((((......))).((((((((......)).)))((((((......)))))).............)))......)))))).))))...)))))). (-35.10 = -36.54 +   1.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,782,866 – 3,782,985
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.32
Mean single sequence MFE -38.70
Consensus MFE -35.84
Energy contribution -36.04
Covariance contribution 0.20
Combinations/Pair 1.11
Mean z-score -1.28
Structure conservation index 0.93
SVM decision value 0.74
SVM RNA-class probability 0.839202
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3782866 119 + 27905053
CAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGGGCGACUAGGA-AAUUUGCAACAAAGUUGCCAUGGCCGGCUGGAAACCCGAUCUCGGUUCCUGUUUGAAGACGGGUUAGUUAGCUA
..(((((........((.(((((((......))))))).)).((.-(((((......))))).)).)))))((((((.((((((.((((((.......))).)))))))))..)))))). ( -40.60)
>DroSec_CAF1 12303 119 + 1
CAGGCCAAACUAAUGAGCCGUCCAACUUGUUUUGGGCGACUAGGA-AAUUUGCAACAAAGUUGCCUUGGCCGGCUGGAAACCCGAUCUCGGUUCCUGUUUGAAGACGGGUUAGUUAGCUC
..((((((.......((.(((((((......))))))).))....-.....(((((...))))).))))))((((((.((((((.((((((.......))).)))))))))..)))))). ( -40.80)
>DroSim_CAF1 16022 119 + 1
CAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGGGCGACUAGGA-AAUUUGCAACAAAGUUGCCUUGGCCGGCUGGAAACCCGAUCUCGGUUCCUGUUUGAAGACGGGUUAGUUAGCUC
..((((((.......((.(((((((......))))))).))....-.....(((((...))))).))))))((((((.((((((.((((((.......))).)))))))))..)))))). ( -40.50)
>DroEre_CAF1 2654 120 + 1
CAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGGGGGAUUAGGAAAACUUGCAACAAAGUUGCCAUGGCCAGCAAGAAACCCGAUCUCGGUUCCUGUUUGAAGACGGGUUAGUUAGCUC
..(((..((((((((((((..((((......))))(((((..((....((((((((...)))((....))..)))))...))..))))))))))(((((....)))))))))))).))). ( -35.60)
>DroYak_CAF1 16022 119 + 1
CAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGG-GGACUGGAAAAAUGUGCAACAAAGUUGCCAUGGCCAGCAAGAAACCCGAUCUCGGUUCCUGUUUGAAGACGGGUUAGUUAGCUC
..(((..(((((((((((((...(((..(((((..-.(.((((....(((.(((((...))))))))..)))))..)))))..).)).))))))(((((....)))))))))))).))). ( -36.00)
>consensus
CAGGCCAAACUAAUGAGCCGUCCGACUUGUUUUGGGCGACUAGGA_AAUUUGCAACAAAGUUGCCAUGGCCGGCUGGAAACCCGAUCUCGGUUCCUGUUUGAAGACGGGUUAGUUAGCUC
..(((((........((.(((((((......))))))).))..........(((((...)))))..)))))((((((.((((((.((((((.......))).)))))))))..)))))). (-35.84 = -36.04 +   0.20)

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 10:05:16 2006