Locus 2158

Sequence ID X_DroMel_CAF1
Location 5,855,362 – 5,855,474
Length 112
Max. P 0.644155
window3498 window3499

overview

Window 8

Location 5,855,362 – 5,855,474
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 89.04
Mean single sequence MFE -32.65
Consensus MFE -24.67
Energy contribution -25.43
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.76
SVM decision value 0.23
SVM RNA-class probability 0.644155
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5855362 112 + 22224390
GGCACUCGACUCGUGGGGUCGCAAGAAAUCGGGCAAAACAAGUGCGAUUCCAAGUACCUCGAAUCGAAAUCGAAAUCGAAAUCCCAAUCCCAAUCGAGUCCAUGUCAAGUGG
((((...(((((((((((((....))....(((........((((........)))).((((.(((....)))..))))...)))..)))))..))))))..))))...... ( -34.30)
>DroSec_CAF1 60602 107 + 1
GGCACUCGACUCGUGGGGUCGCGGCAAAUCGGGCAAAACAAGUGCGAUUCCAAGUGCCUCC-----AAAUCGAAAUCGAAAUCCCAAUCCCAAUCGAGUCCAUGUCAAGUGG
((((...((((((((((((...(((((((((.((.......)).))))).....))))...-----...(((....))).......))))))..))))))..))))...... ( -33.00)
>DroSim_CAF1 63262 107 + 1
GGCACUCGACUCGUGGGGUCGCGGCAAAUCGGGCAAAACAAGUGCGAUUCCAAGUGCCUCC-----AAAUCGAAAUCGAAAUCCCAAUCCCAAUCGAGUCCAUGUCAAGUGG
((((...((((((((((((...(((((((((.((.......)).))))).....))))...-----...(((....))).......))))))..))))))..))))...... ( -33.00)
>DroEre_CAF1 59373 102 + 1
GGCACUCGACUCAUGGGGGCGCGUGAAAUCGGGCAAAACAAAUGCGAUUCGAA-----UCG-----AAAUCGAAUUCGAAACCGAAAUCCCAAUCGAGUCCAUGUCAAGUGG
((((...(((((.(((((((.((......)).))..........((.((((((-----(((-----....)).)))))))..))...)))))...)))))..))))...... ( -30.30)
>consensus
GGCACUCGACUCGUGGGGUCGCGGCAAAUCGGGCAAAACAAGUGCGAUUCCAAGUGCCUCC_____AAAUCGAAAUCGAAAUCCCAAUCCCAAUCGAGUCCAUGUCAAGUGG
((((...((((((((((((.......(((((.((.......)).)))))....................(((....))).......))))))..))))))..))))...... (-24.67 = -25.43 +   0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,855,362 – 5,855,474
Length 112
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 89.04
Mean single sequence MFE -35.50
Consensus MFE -27.29
Energy contribution -28.54
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.77
SVM decision value 0.05
SVM RNA-class probability 0.557013
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5855362 112 - 22224390
CCACUUGACAUGGACUCGAUUGGGAUUGGGAUUUCGAUUUCGAUUUCGAUUCGAGGUACUUGGAAUCGCACUUGUUUUGCCCGAUUUCUUGCGACCCCACGAGUCGAGUGCC
.((((((((.(((..(((...(..(((((((((((((((((((.......)))))))...)))))))(((.......))))))))..)...)))..)))...)))))))).. ( -39.00)
>DroSec_CAF1 60602 107 - 1
CCACUUGACAUGGACUCGAUUGGGAUUGGGAUUUCGAUUUCGAUUU-----GGAGGCACUUGGAAUCGCACUUGUUUUGCCCGAUUUGCCGCGACCCCACGAGUCGAGUGCC
.((((((((.(((..(((....((((((((....(((...((((((-----.(((...))).))))))...))).....))))))))....)))..)))...)))))))).. ( -35.10)
>DroSim_CAF1 63262 107 - 1
CCACUUGACAUGGACUCGAUUGGGAUUGGGAUUUCGAUUUCGAUUU-----GGAGGCACUUGGAAUCGCACUUGUUUUGCCCGAUUUGCCGCGACCCCACGAGUCGAGUGCC
.((((((((.(((..(((....((((((((....(((...((((((-----.(((...))).))))))...))).....))))))))....)))..)))...)))))))).. ( -35.10)
>DroEre_CAF1 59373 102 - 1
CCACUUGACAUGGACUCGAUUGGGAUUUCGGUUUCGAAUUCGAUUU-----CGA-----UUCGAAUCGCAUUUGUUUUGCCCGAUUUCACGCGCCCCCAUGAGUCGAGUGCC
.((((((((((((...((.....((..((((.(((((((.((....-----)))-----))))))..(((.......)))))))..))...))...))))..)))))))).. ( -32.80)
>consensus
CCACUUGACAUGGACUCGAUUGGGAUUGGGAUUUCGAUUUCGAUUU_____CGAGGCACUUGGAAUCGCACUUGUUUUGCCCGAUUUCCCGCGACCCCACGAGUCGAGUGCC
.((((((((.(((..(((...(((((((((....(((...((((((................))))))...))).....)))))))))...)))..)))...)))))))).. (-27.29 = -28.54 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:32 2006