Locus 2605

Sequence ID X_DroMel_CAF1
Location 6,993,524 – 6,993,724
Length 200
Max. P 0.978523
window4263 window4264 window4265

overview

Window 3

Location 6,993,524 – 6,993,644
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -43.40
Consensus MFE -43.31
Energy contribution -42.87
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -1.44
Structure conservation index 1.00
SVM decision value 0.15
SVM RNA-class probability 0.606014
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993524 120 + 22224390
GGGCACGUGUUUGGUCAUCAAGAGGGAUUUUCAUGGCAGAAGAGGUCCUGCCUUCUGACUUCCUUCGAUUGGAUUAUUGGCGCUGCUCGGUGGGCGUUUACAACACUUGUUGAGCAGUGG
..((.((.(((..(((.....((((((...(((.(((((........)))))...)))..)))))))))..)))...))))(((((((((..((.((.....)).))..))))))))).. ( -44.00)
>DroSec_CAF1 15928 120 + 1
GGGCACGUGUUUGGUCAUCAAGAGGGAUUUCCAUGGCAGAAGAGGUCCUGCCUUCUGACUUCCUUCGAUUGGAUUAUUGGCGCUGCUCGGAGGGCGUUUACGACACUUGUUGAGCAGUGG
..((.((.(((..(((.....((((((..((...(((((........)))))....))..)))))))))..)))...))))(((((((((..((.(((...))).))..))))))))).. ( -41.60)
>DroSim_CAF1 1032 120 + 1
GGGCACGUGUUUGGUCAUCAAGAGGGAUUUCCAUGGCAGAAGAGGUCCUGCCUUCUGACUUCCUUCGAUUGGAUUAUUGGCGCUGCUCGGUGGGCGUUUACGACACUUGUUGAGCAGUGG
..((.((.(((..(((.....((((((..((...(((((........)))))....))..)))))))))..)))...))))(((((((((..((.(((...))).))..))))))))).. ( -44.60)
>consensus
GGGCACGUGUUUGGUCAUCAAGAGGGAUUUCCAUGGCAGAAGAGGUCCUGCCUUCUGACUUCCUUCGAUUGGAUUAUUGGCGCUGCUCGGUGGGCGUUUACGACACUUGUUGAGCAGUGG
..((.((.(((..(((.....((((((..((...(((((........)))))....))..)))))))))..)))...))))(((((((((..((.(((...))).))..))))))))).. (-43.31 = -42.87 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,993,604 – 6,993,724
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -36.50
Consensus MFE -35.55
Energy contribution -35.33
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.59
Structure conservation index 0.97
SVM decision value 1.82
SVM RNA-class probability 0.978523
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993604 120 + 22224390
CGCUGCUCGGUGGGCGUUUACAACACUUGUUGAGCAGUGGUGCAUUUGUAUUUAUCUUUUAUUACAUUUAUUUUAUGCCCUGCCAUUGAUGGUGGCGCACUGAGAAUAAAUUUCAGCUCA
((((((((((..((.((.....)).))..))))))))))(.((...((((............))))((((((((.(((.(..(((....)))..).)))...)))))))).....)).). ( -38.00)
>DroSec_CAF1 16008 120 + 1
CGCUGCUCGGAGGGCGUUUACGACACUUGUUGAGCAGUGGUGCAUUUGUAUUUAUCUUUUAUUACAUUUAUUUUAUGCCCUGCCAUUGAUGGUGGCGCACUGAGAAAAAAUGUUAACUCA
((((((((((..((.(((...))).))..))))))))))((((....))))............((((((.((((.(((.(..(((....)))..).)))...)))).))))))....... ( -34.20)
>DroSim_CAF1 1112 119 + 1
CGCUGCUCGGUGGGCGUUUACGACACUUGUUGAGCAGUGGUGCAUUUGUAUUUAUCUUUUAUUACAUUUAU-UUAUGCCCUGCCAUUGAUGGUGGCGCACUGAGAAAAAAUUUCAACUCA
((((((((((..((.(((...))).))..))))))))))((((...((((............)))).....-....(((..((((....)))))))))))(((((.....)))))..... ( -37.30)
>consensus
CGCUGCUCGGUGGGCGUUUACGACACUUGUUGAGCAGUGGUGCAUUUGUAUUUAUCUUUUAUUACAUUUAUUUUAUGCCCUGCCAUUGAUGGUGGCGCACUGAGAAAAAAUUUCAACUCA
((((((((((..((.(((...))).))..))))))))))((((...((((............))))..........(((..((((....))))))))))).(((............))). (-35.55 = -35.33 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,993,604 – 6,993,724
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -27.00
Consensus MFE -25.40
Energy contribution -25.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.94
SVM decision value 0.10
SVM RNA-class probability 0.585560
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6993604 120 - 22224390
UGAGCUGAAAUUUAUUCUCAGUGCGCCACCAUCAAUGGCAGGGCAUAAAAUAAAUGUAAUAAAAGAUAAAUACAAAUGCACCACUGCUCAACAAGUGUUGUAAACGCCCACCGAGCAGCG
...((((.........(((.((..((((.......)))).((((..........((((............))))..((((.((((........)))).))))...)))))).))))))). ( -28.30)
>DroSec_CAF1 16008 120 - 1
UGAGUUAACAUUUUUUCUCAGUGCGCCACCAUCAAUGGCAGGGCAUAAAAUAAAUGUAAUAAAAGAUAAAUACAAAUGCACCACUGCUCAACAAGUGUCGUAAACGCCCUCCGAGCAGCG
((((..((....))..))))(((((((.(((....)))...)))..........((((............))))...))))..((((((.....((((.....)))).....)))))).. ( -26.10)
>DroSim_CAF1 1112 119 - 1
UGAGUUGAAAUUUUUUCUCAGUGCGCCACCAUCAAUGGCAGGGCAUAA-AUAAAUGUAAUAAAAGAUAAAUACAAAUGCACCACUGCUCAACAAGUGUCGUAAACGCCCACCGAGCAGCG
((((..((....))..))))(((((((.(((....)))...)))....-.....((((............))))...))))..((((((.....((((.....)))).....)))))).. ( -26.60)
>consensus
UGAGUUGAAAUUUUUUCUCAGUGCGCCACCAUCAAUGGCAGGGCAUAAAAUAAAUGUAAUAAAAGAUAAAUACAAAUGCACCACUGCUCAACAAGUGUCGUAAACGCCCACCGAGCAGCG
((((............))))(((((((.(((....)))...)))..........((((............))))...))))..((((((.....((((.....)))).....)))))).. (-25.40 = -25.40 +   0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:58 2006