Locus 4049

Sequence ID 3R_DroMel_CAF1
Location 11,042,244 – 11,042,364
Length 120
Max. P 0.835995
window6483 window6484

overview

Window 3

Location 11,042,244 – 11,042,364
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -50.07
Consensus MFE -48.65
Energy contribution -48.77
Covariance contribution 0.11
Combinations/Pair 1.02
Mean z-score -1.91
Structure conservation index 0.97
SVM decision value 0.73
SVM RNA-class probability 0.835995
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11042244 120 + 27905053
GUCCGCCUGGACACUUGGUGAAAGUUUGCGCUUGGUGCUGCUUGUUCGUCGCACGGGUUGCUUGCUUUUUGGCAAGUCGCAGGCCACAGCGGCAGAGUGCAGGCGAUUGUCCUGUUUGUA
((((....))))((..((..(..((((((((((..(((((((.((..(((...(((.(((((........))))).)))..))).)))))))))))))))))))..)..))..))..... ( -45.40)
>DroSec_CAF1 4993 120 + 1
GUCCGCCUGGACACUUGGCGAAAGUUUGCGCUUGGUGCUGCUUGUGCGUCGCACGGGUUGCUUGCUUUUUGGCAAGUCGCAGGCCACAGCGGCAGAGUGCAGGCGAUUGUCCUGUUUGUA
((((....))))((..(((((..((((((((((..(((((((.(((.(((...(((.(((((........))))).)))..)))))))))))))))))))))))..)))))..))..... ( -52.40)
>DroSim_CAF1 5013 120 + 1
GUCCGCCUGGACACUUGGCGAAAGUUUGCGCUUGGUGCUGCUUGUGCGUCGCACGGGUUGCUUGCUUUUUGGCAAGUCGCAGGCCACAGCGGCAGAGUGCAGGCGAUUGUCCUGUUUGUA
((((....))))((..(((((..((((((((((..(((((((.(((.(((...(((.(((((........))))).)))..)))))))))))))))))))))))..)))))..))..... ( -52.40)
>consensus
GUCCGCCUGGACACUUGGCGAAAGUUUGCGCUUGGUGCUGCUUGUGCGUCGCACGGGUUGCUUGCUUUUUGGCAAGUCGCAGGCCACAGCGGCAGAGUGCAGGCGAUUGUCCUGUUUGUA
((((....))))((..(((((..((((((((((..(((((((.(((.(((...(((.(((((........))))).)))..)))))))))))))))))))))))..)))))..))..... (-48.65 = -48.77 +   0.11)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 4

Location 11,042,244 – 11,042,364
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -37.30
Consensus MFE -36.03
Energy contribution -36.37
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.97
SVM decision value 0.32
SVM RNA-class probability 0.689397
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11042244 120 - 27905053
UACAAACAGGACAAUCGCCUGCACUCUGCCGCUGUGGCCUGCGACUUGCCAAAAAGCAAGCAACCCGUGCGACGAACAAGCAGCACCAAGCGCAAACUUUCACCAAGUGUCCAGGCGGAC
..............(((((((.((..(((.(((.(((.(((((.(((((......))))))....((.....)).....))))..))))))))).((((.....)))))).))))))).. ( -34.30)
>DroSec_CAF1 4993 120 - 1
UACAAACAGGACAAUCGCCUGCACUCUGCCGCUGUGGCCUGCGACUUGCCAAAAAGCAAGCAACCCGUGCGACGCACAAGCAGCACCAAGCGCAAACUUUCGCCAAGUGUCCAGGCGGAC
..............(((((((((((..((((((.(((.(((((.(((((......)))))).....((((...))))..))))..))))))).........))..))))..))))))).. ( -38.80)
>DroSim_CAF1 5013 120 - 1
UACAAACAGGACAAUCGCCUGCACUCUGCCGCUGUGGCCUGCGACUUGCCAAAAAGCAAGCAACCCGUGCGACGCACAAGCAGCACCAAGCGCAAACUUUCGCCAAGUGUCCAGGCGGAC
..............(((((((((((..((((((.(((.(((((.(((((......)))))).....((((...))))..))))..))))))).........))..))))..))))))).. ( -38.80)
>consensus
UACAAACAGGACAAUCGCCUGCACUCUGCCGCUGUGGCCUGCGACUUGCCAAAAAGCAAGCAACCCGUGCGACGCACAAGCAGCACCAAGCGCAAACUUUCGCCAAGUGUCCAGGCGGAC
..............(((((((.((..(((.(((.(((.(((((.(((((......)))))).....((((...))))..))))..))))))))).((((.....)))))).))))))).. (-36.03 = -36.37 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:44 2006