Locus 6445

Sequence ID X_DroMel_CAF1
Location 16,154,296 – 16,154,452
Length 156
Max. P 0.919958
window10521 window10522

overview

Window 1

Location 16,154,296 – 16,154,412
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.41
Mean single sequence MFE -39.12
Consensus MFE -31.76
Energy contribution -31.80
Covariance contribution 0.04
Combinations/Pair 1.10
Mean z-score -1.85
Structure conservation index 0.81
SVM decision value 1.13
SVM RNA-class probability 0.919958
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16154296 116 - 22224390
AAUG-GGCAGCACAAAGUGCGUUUAUGGGCGCCCUAAAGUGAUGUAACAAUUGCUGCGACCGCAGCA---GCAGCGAAACGCGCGGAAUGGAACGCACGGAACGAUAUCGUAGUAUCGUA
...(-(((.((((...))))(((....)))))))....(((.(((..((..((((((....))))))---((.(((...)))))....))..))))))...(((((((....))))))). ( -38.90)
>DroSec_CAF1 150 117 - 1
AAUGGGGCAGCAAAAAGUGCGUUUAUGGGCGCCCUAAAGUGAUGUAACAAUUGCUGCGACCGCAGCA---GCGGCGAAACGCGCGGAAUGGAACGCACGGAACGAUAUCGUAGUAUCGUA
..((((((.(((.....)))(((....)))))))))..(((.(((..((..((((((....))))))---(((......)))......))..))))))...(((((((....))))))). ( -40.30)
>DroSim_CAF1 935 116 - 1
AAUG-GGCAGCAUAAAGUGCGUUUAUGGGCGCCCUAAAGUGAUGUAACAAUUGCUGCGACCGCAGCA---GCGGCGAAACGCGCGGAAUGGAACGCACGGAACGAUAUCGUAGUAUCGUA
...(-(((.((((...))))(((....)))))))....(((.(((..((..((((((....))))))---(((......)))......))..))))))...(((((((....))))))). ( -38.30)
>DroEre_CAF1 149 113 - 1
AAUG-GGCCGCGAAAAGUGCGUUCAUGGGCGCCGCAAAGUGAUGUAACAAUAGCUGCGACCGCAG------CAGCGGAACGCGCGGAAUGGAACGCACGGAACGGUAUCGUAGUAUCGUA
.(((-(((((......((((((((.((.(((((((...((......))....(((((....))))------).))))..))).)).....))))))))....)))).))))......... ( -42.30)
>DroYak_CAF1 1032 119 - 1
AAUG-GACCGCAAAAAGUGCGUUUAUGGGCGCCGCAAAGUGAUGUAACAAUAGCUGCGACCGCAGCAGCAGCAGCGGAACGGGCGGAAUAGAACGCAUGGAACGGUAUCGUAGUAUCGUA
..((-..((((.....(.(((((....))))))((...((......))....(((((....))))).))....))))..)).(((........))).....(((((((....))))))). ( -35.80)
>consensus
AAUG_GGCAGCAAAAAGUGCGUUUAUGGGCGCCCUAAAGUGAUGUAACAAUUGCUGCGACCGCAGCA___GCAGCGAAACGCGCGGAAUGGAACGCACGGAACGAUAUCGUAGUAUCGUA
................((((((((.....(((......((..(((......((((((....))))))......)))..))..))).....))))))))...(((((((....))))))). (-31.76 = -31.80 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,154,336 – 16,154,452
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.10
Mean single sequence MFE -46.44
Consensus MFE -31.72
Energy contribution -33.52
Covariance contribution 1.80
Combinations/Pair 1.11
Mean z-score -2.86
Structure conservation index 0.68
SVM decision value 0.93
SVM RNA-class probability 0.884924
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16154336 116 - 22224390
AGGGCGCAUGAACGCGACCAUUUAUCCGUUUUGAUGGGGGAAUG-GGCAGCACAAAGUGCGUUUAUGGGCGCCCUAAAGUGAUGUAACAAUUGCUGCGACCGCAGCA---GCAGCGAAAC
(((((((((((((((..((((((..((((....))))..)))))-))).((((...))))))))))..)))))))...((......))..(((((((....))))))---)......... ( -45.30)
>DroSec_CAF1 190 117 - 1
AGGGUGCAUGAACGCGACCAUUUAACCGUUUUGGUGGGGGAAUGGGGCAGCAAAAAGUGCGUUUAUGGGCGCCCUAAAGUGAUGUAACAAUUGCUGCGACCGCAGCA---GCGGCGAAAC
(((((((((((((((..((((((..(((......)))..)))))).)).(((.....)))))))))..)))))))..((..((......))..)).((.((((....---)))))).... ( -44.70)
>DroSim_CAF1 975 116 - 1
AGGCCGCAUGAACGCGACCAUUUAACCGUUUUGGUGGGGGAAUG-GGCAGCAUAAAGUGCGUUUAUGGGCGCCCUAAAGUGAUGUAACAAUUGCUGCGACCGCAGCA---GCGGCGAAAC
..(((.(((((((((..((((((..(((......)))..)))))-)((........))))))))))))))(((.....((......))..(((((((....))))))---).)))..... ( -45.20)
>DroEre_CAF1 189 113 - 1
AAGGCGCAUGAACGCGCCCAUUUAUCCGUUUUGGCCGGGGAAUG-GGCCGCGAAAAGUGCGUUCAUGGGCGCCGCAAAGUGAUGUAACAAUAGCUGCGACCGCAG------CAGCGGAAC
...((.(((((((((((((((((.((((.......)))))))))-))).((.....))))))))))).)).((((...((......))....(((((....))))------).))))... ( -52.70)
>DroYak_CAF1 1072 119 - 1
UAGGCGCAUGAACGCGACCAUUUAUGCGUGCUGGGCGGGGAAUG-GACCGCAAAAAGUGCGUUUAUGGGCGCCGCAAAGUGAUGUAACAAUAGCUGCGACCGCAGCAGCAGCAGCGGAAC
...((.((((((((((........)))(..((..((((......-..))))....))..)))))))).)).((((...((......))....(((((....))))).......))))... ( -44.30)
>consensus
AGGGCGCAUGAACGCGACCAUUUAUCCGUUUUGGUGGGGGAAUG_GGCAGCAAAAAGUGCGUUUAUGGGCGCCCUAAAGUGAUGUAACAAUUGCUGCGACCGCAGCA___GCAGCGAAAC
(((((((((((((((..((((((..((((....))))..))))).)...((.....))))))))))..)))))))...((..(((......((((((....))))))......)))..)) (-31.72 = -33.52 +   1.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:55 2006