Locus 6618

Sequence ID 3R_DroMel_CAF1
Location 17,421,566 – 17,421,679
Length 113
Max. P 0.999571
window10773 window10774

overview

Window 3

Location 17,421,566 – 17,421,679
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 96.55
Mean single sequence MFE -45.12
Consensus MFE -42.74
Energy contribution -43.22
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -2.19
Structure conservation index 0.95
SVM decision value 3.52
SVM RNA-class probability 0.999335
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17421566 113 + 27905053
GAGACAACCGACGCAACGUCCCCCCAAUGAGGUCCCCACUGAAAUCACAGUGGGGAGAAUUCGGAGGUUUGGACGUGCUCUAAAGGUGCAGUUUGUGGUCUAUGCACGUCCGC
(.(((....((.(((.(((((..((..((((.(((((((((......)))))))))...))))..))...)))))))))).....(((((............))))))))).. ( -43.60)
>DroSec_CAF1 25625 113 + 1
GAGACAACCGACGCAACGUCCCCCCAAUGAGGCCCCCACUGAAAUCACAGUGGGGAGAAUUCGGAGGGUUGGACGUGCUCUAAAGGUGCAGUUUGUGGUCUCUGCACGUCCGC
(.(((....((.(((.(((((.(((..((((..((((((((......))))))))....))))..)))..)))))))))).....((((((..........)))))))))).. ( -47.70)
>DroSim_CAF1 23009 113 + 1
GAGACAACCGACGCAACGUCCCCCCAAUGAGGCCCCCACUGAAAUCACAGUGGGGAGAAUUCGGAGGGUUGGACGUGCUCUAAAGGUGCAGUUUGUGGUCUCUGCACGUCCGC
(.(((....((.(((.(((((.(((..((((..((((((((......))))))))....))))..)))..)))))))))).....((((((..........)))))))))).. ( -47.70)
>DroEre_CAF1 24514 113 + 1
GAGACAACCGACGCAACGUCCCCCCAAUGAGGCCCCCACUGAAAUCACAGUGGGGAGAAUUCGGAGGGUUGGACGUGCUCUAAAGGUGCAGUUUGUGGUCUCUGCACGUCCGC
(.(((....((.(((.(((((.(((..((((..((((((((......))))))))....))))..)))..)))))))))).....((((((..........)))))))))).. ( -47.70)
>DroYak_CAF1 22722 111 + 1
GAGACAACCGACGCAACGUCCCCCCAAUGGGGACCC--CUGAAAUAAUAGUGGGGAGAAUUCGUAGGGUUGGACGUGCUCUAAAGGUGCAGUUUGUGGUCUCUGCACGUCCGC
(.(((....((.(((.(((((.(((.(((((..(((--(............))))....))))).)))..)))))))))).....((((((..........)))))))))).. ( -38.90)
>consensus
GAGACAACCGACGCAACGUCCCCCCAAUGAGGCCCCCACUGAAAUCACAGUGGGGAGAAUUCGGAGGGUUGGACGUGCUCUAAAGGUGCAGUUUGUGGUCUCUGCACGUCCGC
(.(((....((.(((.(((((.(((..((((..((((((((......))))))))....))))..)))..)))))))))).....((((((..........)))))))))).. (-42.74 = -43.22 +   0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,421,566 – 17,421,679
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 96.55
Mean single sequence MFE -44.86
Consensus MFE -42.08
Energy contribution -42.80
Covariance contribution 0.72
Combinations/Pair 1.06
Mean z-score -2.34
Structure conservation index 0.94
SVM decision value 3.73
SVM RNA-class probability 0.999571
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17421566 113 - 27905053
GCGGACGUGCAUAGACCACAAACUGCACCUUUAGAGCACGUCCAAACCUCCGAAUUCUCCCCACUGUGAUUUCAGUGGGGACCUCAUUGGGGGGACGUUGCGUCGGUUGUCUC
..((((((((.((((..............))))..))))))))...(((((((....(((((((((......))))))))).....)))))))((((...))))......... ( -45.04)
>DroSec_CAF1 25625 113 - 1
GCGGACGUGCAGAGACCACAAACUGCACCUUUAGAGCACGUCCAACCCUCCGAAUUCUCCCCACUGUGAUUUCAGUGGGGGCCUCAUUGGGGGGACGUUGCGUCGGUUGUCUC
((.(((((((((..........)))))).......((((((....((((((((....(((((((((......))))))))).....))))))))))).)))))).))...... ( -47.30)
>DroSim_CAF1 23009 113 - 1
GCGGACGUGCAGAGACCACAAACUGCACCUUUAGAGCACGUCCAACCCUCCGAAUUCUCCCCACUGUGAUUUCAGUGGGGGCCUCAUUGGGGGGACGUUGCGUCGGUUGUCUC
((.(((((((((..........)))))).......((((((....((((((((....(((((((((......))))))))).....))))))))))).)))))).))...... ( -47.30)
>DroEre_CAF1 24514 113 - 1
GCGGACGUGCAGAGACCACAAACUGCACCUUUAGAGCACGUCCAACCCUCCGAAUUCUCCCCACUGUGAUUUCAGUGGGGGCCUCAUUGGGGGGACGUUGCGUCGGUUGUCUC
((.(((((((((..........)))))).......((((((....((((((((....(((((((((......))))))))).....))))))))))).)))))).))...... ( -47.30)
>DroYak_CAF1 22722 111 - 1
GCGGACGUGCAGAGACCACAAACUGCACCUUUAGAGCACGUCCAACCCUACGAAUUCUCCCCACUAUUAUUUCAG--GGGUCCCCAUUGGGGGGACGUUGCGUCGGUUGUCUC
((.(((((((((..........)))))).......((((((((..(((((........((((............)--))).......)))))))))).)))))).))...... ( -37.36)
>consensus
GCGGACGUGCAGAGACCACAAACUGCACCUUUAGAGCACGUCCAACCCUCCGAAUUCUCCCCACUGUGAUUUCAGUGGGGGCCUCAUUGGGGGGACGUUGCGUCGGUUGUCUC
((.(((((((((..........)))))).......((((((((..............(((((((((......)))))))))(((.....)))))))).)))))).))...... (-42.08 = -42.80 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:01 2006