Locus 867

Sequence ID X_DroMel_CAF1
Location 2,445,815 – 2,445,959
Length 144
Max. P 0.871583
window1405 window1406

overview

Window 5

Location 2,445,815 – 2,445,919
Length 104
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.15
Mean single sequence MFE -35.09
Consensus MFE -33.91
Energy contribution -33.36
Covariance contribution -0.55
Combinations/Pair 1.14
Mean z-score -1.07
Structure conservation index 0.97
SVM decision value 0.87
SVM RNA-class probability 0.871583
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2445815 104 + 22224390
GCCACCCCC------------CUCACUUUCGACGCCCUUGGACCGCCUAUUAGCACAUUUCGGUUAACAGCAGUUGUUGUCGCCGUGUGUGUACAUA----UGUGCACAGUGGCGGGCAA
(((......------------.((......))((((.(((...(((.(((..((((((..((((..(((((....))))).)))).))))))..)))----.)))..))).))))))).. ( -33.30)
>DroSec_CAF1 6655 120 + 1
GCCACCCCCUCACCCCACCCCCCCCUUUUCGACGCCCUUGGACCGCCUUUUAGCACAUUUCGGUUAGCAGCACUCGUUGUCGCCGUGUGUGUACAUAUGUAUGUGCACAGCGGCGGGCAA
.................................((((...(((((...............))))).(((((....))))).(((((.(((((((((....)))))))))))))))))).. ( -35.96)
>DroSim_CAF1 8846 117 + 1
GCCACCCCCUCACCC---ACCCCCCUUUUCGACGCCCUUGAACCGCCUAUUAGCACAUUUCGGUUAGCAGCACUCGUUGUCGCCGUGUGUGUGCAUAUGUAUGUGCACAGCGGCGGGCAA
(((............---.........(((((.....))))).((((.....(((((...((((..(((((....))))).)))))))))(((((((....)))))))...))))))).. ( -36.00)
>consensus
GCCACCCCCUCACCC____CCCCCCUUUUCGACGCCCUUGGACCGCCUAUUAGCACAUUUCGGUUAGCAGCACUCGUUGUCGCCGUGUGUGUACAUAUGUAUGUGCACAGCGGCGGGCAA
.................................((((...(((((...............))))).(((((....))))).(((((.(((((((((....)))))))))))))))))).. (-33.91 = -33.36 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,445,843 – 2,445,959
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.35
Mean single sequence MFE -36.17
Consensus MFE -29.44
Energy contribution -29.33
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -1.53
Structure conservation index 0.81
SVM decision value 0.23
SVM RNA-class probability 0.643318
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2445843 116 + 22224390
GACCGCCUAUUAGCACAUUUCGGUUAACAGCAGUUGUUGUCGCCGUGUGUGUACAUA----UGUGCACAGUGGCGGGCAAGAAAGUAGGUCCUAAGUACAGAGAUUUCCAAUAAUUGCGA
..(((((.............((((..(((((....))))).))))..(((((((...----.)))))))..)))))((((......(((((((......)).))))).......)))).. ( -34.02)
>DroSec_CAF1 6695 108 + 1
GACCGCCUUUUAGCACAUUUCGGUUAGCAGCACUCGUUGUCGCCGUGUGUGUACAUAUGUAUGUGCACAGCGGCGGGCAAGAAAGUAGGA-CUAAGU---------GCAAGUCAUUAU--
(((.((..(((((..(.((((.(((.(((((....)))))((((((.(((((((((....))))))))))))))))))..))))...)..-))))).---------))..))).....-- ( -36.10)
>DroSim_CAF1 8883 117 + 1
AACCGCCUAUUAGCACAUUUCGGUUAGCAGCACUCGUUGUCGCCGUGUGUGUGCAUAUGUAUGUGCACAGCGGCGGGCAAGAAAGUAGGA-CUAAGUACACUGAUUGCGAGUAAUUAU--
..(((((.....(((((...((((..(((((....))))).)))))))))(((((((....)))))))...)))))((((...(((.(..-.......))))..))))..........-- ( -38.40)
>consensus
GACCGCCUAUUAGCACAUUUCGGUUAGCAGCACUCGUUGUCGCCGUGUGUGUACAUAUGUAUGUGCACAGCGGCGGGCAAGAAAGUAGGA_CUAAGUACA__GAUUGCAAGUAAUUAU__
..(((((.............((((..(((((....))))).))))..(((((((((....)))))))))..)))))............................................ (-29.44 = -29.33 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:47 2006