Locus 5365

Sequence ID X_DroMel_CAF1
Location 13,962,195 – 13,962,314
Length 119
Max. P 0.961113
window8709 window8710

overview

Window 9

Location 13,962,195 – 13,962,314
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.73
Mean single sequence MFE -45.30
Consensus MFE -34.79
Energy contribution -36.35
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -2.84
Structure conservation index 0.77
SVM decision value 1.52
SVM RNA-class probability 0.961113
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13962195 119 + 22224390
AAAAAGCGCAGGCGGGUGGGCGCCGUUGGCCCCAACGCGAGAGUCAAGAACGUAAAGCAUAAUAAAAAGUCGUGCCUUACGUGCAGCAGUUGGAAAGCCCCCCCCCGAAUGCGCCC-ACC
.....(((((..((((.(((((((...))).(((((((....))...(.((((((.(((..((.....))..))).)))))).)....)))))...))))...))))..)))))..-... ( -47.30)
>DroSec_CAF1 13722 117 + 1
AAAAAGCGCAGGCGGGUGGGCGCCGUUGGCCCCAACGCGAGAGCCAAGAACGUAAAGCAUAAUAAAAAGUCGUGCCUUACGUGCAGCAGUUGGGAAGCCC---CCCGAAUGUACCCCCCC
.......(((..((((.(((((((...)))((((((((....))...(.((((((.(((..((.....))..))).)))))).)....))))))..))))---))))..)))........ ( -47.70)
>DroSim_CAF1 14178 116 + 1
AAAAAGCGCAGGCGGGUGGGCGCCGUUGGCCCCAACGCGAGAGCCAAGAACGUAAAGCAUAAUAAAAAGUCGUGCCUUACGUGCAGCAGUUGGGAAGCCC---CCCGAAUGUACCC-CCC
.......(((..((((.(((((((...)))((((((((....))...(.((((((.(((..((.....))..))).)))))).)....))))))..))))---))))..)))....-... ( -47.70)
>DroYak_CAF1 14093 114 + 1
AAUAAGCGCAGGCGGGUGGGCGCCGUUAGCCCCUUCGCGAGAGCCAAGAACGUAAAGCAUAAUAAAAAGUCUUGCCUUACGUGAAGCUUUUUGGAAUCCC---CCC---UCCACCGCCNN
.....(((..((.(((.(((..(((..(((..(((.((....)).))).((((((.(((..((.....))..))).))))))...)))...)))...)))---)))---.))..)))... ( -38.50)
>consensus
AAAAAGCGCAGGCGGGUGGGCGCCGUUGGCCCCAACGCGAGAGCCAAGAACGUAAAGCAUAAUAAAAAGUCGUGCCUUACGUGCAGCAGUUGGGAAGCCC___CCCGAAUGCACCC_CCC
.......(((..((((.((((((.....))((((((((....)).....((((((.(((..((.....))..))).))))))......))))))..))))...))))..)))........ (-34.79 = -36.35 +   1.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,962,195 – 13,962,314
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.73
Mean single sequence MFE -46.63
Consensus MFE -37.17
Energy contribution -38.30
Covariance contribution 1.13
Combinations/Pair 1.06
Mean z-score -1.96
Structure conservation index 0.80
SVM decision value 0.81
SVM RNA-class probability 0.856732
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13962195 119 - 22224390
GGU-GGGCGCAUUCGGGGGGGGGCUUUCCAACUGCUGCACGUAAGGCACGACUUUUUAUUAUGCUUUACGUUCUUGACUCUCGCGUUGGGGCCAACGGCGCCCACCCGCCUGCGCUUUUU
(((-((((((...(((((((.(((.........))).)((((((((((..(.......)..))))))))))......))))))(((((....)))))))))))))).((....))..... ( -50.60)
>DroSec_CAF1 13722 117 - 1
GGGGGGGUACAUUCGGG---GGGCUUCCCAACUGCUGCACGUAAGGCACGACUUUUUAUUAUGCUUUACGUUCUUGGCUCUCGCGUUGGGGCCAACGGCGCCCACCCGCCUGCGCUUUUU
.((((((..((..((((---((((..((((((.((.((((((((((((..(.......)..)))))))))).....))....))))))))(((...))))))).))))..))..)))))) ( -47.70)
>DroSim_CAF1 14178 116 - 1
GGG-GGGUACAUUCGGG---GGGCUUCCCAACUGCUGCACGUAAGGCACGACUUUUUAUUAUGCUUUACGUUCUUGGCUCUCGCGUUGGGGCCAACGGCGCCCACCCGCCUGCGCUUUUU
.((-(((..((..((((---((((..((((((.((.((((((((((((..(.......)..)))))))))).....))....))))))))(((...))))))).))))..))..))))). ( -47.30)
>DroYak_CAF1 14093 114 - 1
NNGGCGGUGGA---GGG---GGGAUUCCAAAAAGCUUCACGUAAGGCAAGACUUUUUAUUAUGCUUUACGUUCUUGGCUCUCGCGAAGGGGCUAACGGCGCCCACCCGCCUGCGCUUAUU
.....((((.(---((.---(((...........((((((((((((((.((.......)).)))))))))).....((....))))))((((.......)))).))).))).)))).... ( -40.90)
>consensus
GGG_GGGUACAUUCGGG___GGGCUUCCCAACUGCUGCACGUAAGGCACGACUUUUUAUUAUGCUUUACGUUCUUGGCUCUCGCGUUGGGGCCAACGGCGCCCACCCGCCUGCGCUUUUU
.....((((((..((((...((((................((((((((..(.......)..))))))))((..((((((((......))))))))..)))))).))))..)))))).... (-37.17 = -38.30 +   1.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:15 2006