Locus 1762

Sequence ID 2L_DroMel_CAF1
Location 4,820,757 – 4,820,887
Length 130
Max. P 0.995837
window2832 window2833 window2834

overview

Window 2

Location 4,820,757 – 4,820,847
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 96.22
Mean single sequence MFE -28.84
Consensus MFE -28.48
Energy contribution -28.48
Covariance contribution 0.00
Combinations/Pair 1.07
Mean z-score -1.71
Structure conservation index 0.99
SVM decision value 2.62
SVM RNA-class probability 0.995837
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4820757 90 + 22407834
UGUACAGUUACCGCUGGGCAAUGGCAACGUGCAAAACAAAAGCCGAACUCCUCAUCCGUCUCACCGAGGAGUUGGAGUGAGAGAGUGGCA
(((.((((....)))).(((.((....)))))...)))...(((..((((((((((((.(((......))).)))).)))).))))))). ( -30.90)
>DroSec_CAF1 7325 90 + 1
UGUACAGUUACCGCUGGGCAAUGGCAACGUGCAAAACAAAAGCCGAACUCCUCGUCCGUCUCACCAAGGAGUUGGAGUGAGAGAGUAGCA
(((.((((....)))).(((.((....)))))...)))...((...((((((((((((.(((......))).)))).)))).)))).)). ( -27.10)
>DroSim_CAF1 7455 90 + 1
UGUACAGUUACCGCUGGGCAAUGGCAACGUGCAAAACAAAAGCCGAACUCCUCGUCCGUCUCACCAAGGAGUUGGAGUGAGAGAGUGGCA
(((.((((....)))).(((.((....)))))...)))...(((..((((((((((((.(((......))).)))).)))).))))))). ( -30.50)
>DroEre_CAF1 7529 90 + 1
UGUACAGUUACCGCUGGGCAAUGGCAACGUGCAAAAUAAAAGCCGAACUCCUCAUCCGUCUCAUCAAGAAGUUGGAGUGAGAGAGUGGCC
....((((....)))).(((.((....))))).........(((..((((((((((((.((........)).)))).)))).))))))). ( -25.70)
>DroYak_CAF1 7728 90 + 1
UGUACAGUUACCGCUGGGCAAUGGCAACGUGCAAAACAAAAGCCGAACUCCUCAUCCGUCUCAUCAAGGAGUUGGAGUGAGAGAGUGGCC
(((.((((....)))).(((.((....)))))...)))...(((..((((((((((((.(((......))).)))).)))).))))))). ( -30.00)
>consensus
UGUACAGUUACCGCUGGGCAAUGGCAACGUGCAAAACAAAAGCCGAACUCCUCAUCCGUCUCACCAAGGAGUUGGAGUGAGAGAGUGGCA
(((.((((....)))).(((.((....)))))...)))...(((..((((((((((((.(((......))).)))).)))).))))))). (-28.48 = -28.48 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,820,757 – 4,820,847
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 96.22
Mean single sequence MFE -27.32
Consensus MFE -26.72
Energy contribution -26.80
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.32
Structure conservation index 0.98
SVM decision value 1.17
SVM RNA-class probability 0.926217
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4820757 90 - 22407834
UGCCACUCUCUCACUCCAACUCCUCGGUGAGACGGAUGAGGAGUUCGGCUUUUGUUUUGCACGUUGCCAUUGCCCAGCGGUAACUGUACA
.(((((((.((((.(((..(((......)))..)))))))))))..)))........((((.((((((.((....)).)))))))))).. ( -28.80)
>DroSec_CAF1 7325 90 - 1
UGCUACUCUCUCACUCCAACUCCUUGGUGAGACGGACGAGGAGUUCGGCUUUUGUUUUGCACGUUGCCAUUGCCCAGCGGUAACUGUACA
.(((((((.(((..(((..(((......)))..))).)))))))..)))........((((.((((((.((....)).)))))))))).. ( -24.70)
>DroSim_CAF1 7455 90 - 1
UGCCACUCUCUCACUCCAACUCCUUGGUGAGACGGACGAGGAGUUCGGCUUUUGUUUUGCACGUUGCCAUUGCCCAGCGGUAACUGUACA
.(((((((.(((..(((..(((......)))..))).)))))))..)))........((((.((((((.((....)).)))))))))).. ( -26.40)
>DroEre_CAF1 7529 90 - 1
GGCCACUCUCUCACUCCAACUUCUUGAUGAGACGGAUGAGGAGUUCGGCUUUUAUUUUGCACGUUGCCAUUGCCCAGCGGUAACUGUACA
((((((((.((((.(((..(((......)))..)))))))))))..)))).......((((.((((((.((....)).)))))))))).. ( -27.40)
>DroYak_CAF1 7728 90 - 1
GGCCACUCUCUCACUCCAACUCCUUGAUGAGACGGAUGAGGAGUUCGGCUUUUGUUUUGCACGUUGCCAUUGCCCAGCGGUAACUGUACA
((((((((.((((.(((..(((......)))..)))))))))))..)))).......((((.((((((.((....)).)))))))))).. ( -29.30)
>consensus
UGCCACUCUCUCACUCCAACUCCUUGGUGAGACGGAUGAGGAGUUCGGCUUUUGUUUUGCACGUUGCCAUUGCCCAGCGGUAACUGUACA
.(((((((.((((.(((..(((......)))..)))))))))))..)))........((((.((((((.((....)).)))))))))).. (-26.72 = -26.80 +   0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,820,787 – 4,820,887
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 92.50
Mean single sequence MFE -32.68
Consensus MFE -25.92
Energy contribution -26.56
Covariance contribution 0.64
Combinations/Pair 1.08
Mean z-score -2.07
Structure conservation index 0.79
SVM decision value 1.22
SVM RNA-class probability 0.932748
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4820787 100 + 22407834
GCAAAACAAAAGCCGAACUCCUCAUCCGUCUCACCGAGGAGUUGGAGUGAGAGAGUGGCAGGAAGAGAGCCUUUUCGAUGGGGAUGGCAACACCAGCACG
((....((...(((..((((((((((((.(((......))).)))).)))).)))))))..((((((...))))))..)).((.((....)))).))... ( -32.30)
>DroSec_CAF1 7355 98 + 1
GCAAAACAAAAGCCGAACUCCUCGUCCGUCUCACCAAGGAGUUGGAGUGAGAGAGUAGCAGGAAGAGAGCCU--GCGAUGGGGAUGGCAACACCAGCACG
((..........(((.((((((((((((.(((......))).)))).)))).)))).(((((.......)))--))..)))((.((....)))).))... ( -34.30)
>DroSim_CAF1 7485 100 + 1
GCAAAACAAAAGCCGAACUCCUCGUCCGUCUCACCAAGGAGUUGGAGUGAGAGAGUGGCAGGAAGAGAGCCUUUUCGAUGGGGAUGGCAACACCAGCACG
((....((...(((..((((((((((((.(((......))).)))).)))).)))))))..((((((...))))))..)).((.((....)))).))... ( -31.90)
>DroEre_CAF1 7559 100 + 1
GCAAAAUAAAAGCCGAACUCCUCAUCCGUCUCAUCAAGAAGUUGGAGUGAGAGAGUGGCCGAAAGAGAGCCAUUCCGAUGGGGAUGGCAACACCAACACA
...........((((...((((((((..(((((((((....)))..))))))((((((((....)...))))))).))))))))))))............ ( -33.00)
>DroYak_CAF1 7758 100 + 1
GCAAAACAAAAGCCGAACUCCUCAUCCGUCUCAUCAAGGAGUUGGAGUGAGAGAGUGGCCGAAAGAGAGCCUUUUCGAUGGGGAUGGCAACACCAACGCA
((....((...(((..((((((((((((.(((......))).)))).)))).)))))))((((((......)))))).)).((.((....))))...)). ( -31.90)
>consensus
GCAAAACAAAAGCCGAACUCCUCAUCCGUCUCACCAAGGAGUUGGAGUGAGAGAGUGGCAGGAAGAGAGCCUUUUCGAUGGGGAUGGCAACACCAGCACG
...........(((..((((((((((((.(((......))).)))).)))).))))))).........(((.((((....)))).)))............ (-25.92 = -26.56 +   0.64)

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 10:10:35 2006