Locus 4625

Sequence ID 3L_DroMel_CAF1
Location 13,162,000 – 13,162,115
Length 115
Max. P 0.999585
window7261 window7262

overview

Window 1

Location 13,162,000 – 13,162,115
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 96.90
Mean single sequence MFE -31.70
Consensus MFE -31.70
Energy contribution -31.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 1.00
SVM decision value 2.78
SVM RNA-class probability 0.997011
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13162000 115 + 23771897
AUUUUUUUUUUUCGCCAAACACUUUGACAGUUUUGGGUCAGGCUUCGCUUUGUCUGGCUGCGAUUCUUUCUGGUGAAAGGUGGAUGCCGUUUUUGGGCAAAGUCAUUUAACCUUU
..........((((((...((((..((.((..(((((((((((........)))))))).)))..)).)).))))...))))))((((.......))))................ ( -31.70)
>DroSec_CAF1 13568 112 + 1
AUUUU---UUUUCGCCAAACACUUUGACAGUUUUGGGUCAGGCUUCGCUUUGUCUGGCUGCGAUUCUUUCUGGUGAAAGGUGGAUGCCGUUUUUGGGCAAAGUCAUUUAGCCUUU
.....---..((((((...((((..((.((..(((((((((((........)))))))).)))..)).)).))))...))))))((((.......))))................ ( -31.70)
>DroSim_CAF1 11818 112 + 1
AUUUU---UUUUCGCCAAACACUUUGACAGUUUUGGGUCAGGCUUCGCUUUGUCUGGCUGCGAUUCUUUCUGGUGAAAGGUGGAUGCCGUUUUUGGGCAAAGUCAUUUAGCCUUU
.....---..((((((...((((..((.((..(((((((((((........)))))))).)))..)).)).))))...))))))((((.......))))................ ( -31.70)
>DroEre_CAF1 16975 110 + 1
UU--U---UUUUCGCCAAACACUUUGACAGUUUUGGGUCAGGCUUCGCUUUGUCUGGCUGCGAUUCUUUCUGGUGAAAGGUGGAUGCCGUUUUUGGGCAAAGUCAUUUAGCCUUU
..--.---..((((((...((((..((.((..(((((((((((........)))))))).)))..)).)).))))...))))))((((.......))))................ ( -31.70)
>DroYak_CAF1 12067 110 + 1
CU--U---UUUUCGCCAAACACUUUGACAGUUUUGGGUCAGGCUUCGCUUUGUCUGGCUGCGAUUCUUUCUGGUGAAAGGUGGAUGCCGUUUUUGGGCAAAGUCAUUUAGCCUUU
..--.---..((((((...((((..((.((..(((((((((((........)))))))).)))..)).)).))))...))))))((((.......))))................ ( -31.70)
>consensus
AUUUU___UUUUCGCCAAACACUUUGACAGUUUUGGGUCAGGCUUCGCUUUGUCUGGCUGCGAUUCUUUCUGGUGAAAGGUGGAUGCCGUUUUUGGGCAAAGUCAUUUAGCCUUU
..........((((((...((((..((.((..(((((((((((........)))))))).)))..)).)).))))...))))))((((.......))))................ (-31.70 = -31.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,162,000 – 13,162,115
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 96.90
Mean single sequence MFE -24.70
Consensus MFE -24.56
Energy contribution -24.40
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.99
SVM decision value 3.75
SVM RNA-class probability 0.999585
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13162000 115 - 23771897
AAAGGUUAAAUGACUUUGCCCAAAAACGGCAUCCACCUUUCACCAGAAAGAAUCGCAGCCAGACAAAGCGAAGCCUGACCCAAAACUGUCAAAGUGUUUGGCGAAAAAAAAAAAU
.((((((....))))))(((.(((.(((((......(((((....)))))..((((...........)))).)))((((........))))..)).))))))............. ( -23.90)
>DroSec_CAF1 13568 112 - 1
AAAGGCUAAAUGACUUUGCCCAAAAACGGCAUCCACCUUUCACCAGAAAGAAUCGCAGCCAGACAAAGCGAAGCCUGACCCAAAACUGUCAAAGUGUUUGGCGAAAA---AAAAU
....(((((((.(((((..........(((......(((((....)))))..((((...........)))).))).(((........))))))))))))))).....---..... ( -24.90)
>DroSim_CAF1 11818 112 - 1
AAAGGCUAAAUGACUUUGCCCAAAAACGGCAUCCACCUUUCACCAGAAAGAAUCGCAGCCAGACAAAGCGAAGCCUGACCCAAAACUGUCAAAGUGUUUGGCGAAAA---AAAAU
....(((((((.(((((..........(((......(((((....)))))..((((...........)))).))).(((........))))))))))))))).....---..... ( -24.90)
>DroEre_CAF1 16975 110 - 1
AAAGGCUAAAUGACUUUGCCCAAAAACGGCAUCCACCUUUCACCAGAAAGAAUCGCAGCCAGACAAAGCGAAGCCUGACCCAAAACUGUCAAAGUGUUUGGCGAAAA---A--AA
....(((((((.(((((..........(((......(((((....)))))..((((...........)))).))).(((........))))))))))))))).....---.--.. ( -24.90)
>DroYak_CAF1 12067 110 - 1
AAAGGCUAAAUGACUUUGCCCAAAAACGGCAUCCACCUUUCACCAGAAAGAAUCGCAGCCAGACAAAGCGAAGCCUGACCCAAAACUGUCAAAGUGUUUGGCGAAAA---A--AG
....(((((((.(((((..........(((......(((((....)))))..((((...........)))).))).(((........))))))))))))))).....---.--.. ( -24.90)
>consensus
AAAGGCUAAAUGACUUUGCCCAAAAACGGCAUCCACCUUUCACCAGAAAGAAUCGCAGCCAGACAAAGCGAAGCCUGACCCAAAACUGUCAAAGUGUUUGGCGAAAA___AAAAU
....(((((((.(((((..........(((......(((((....)))))..((((...........)))).))).(((........)))))))))))))))............. (-24.56 = -24.40 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:51 2006