Locus 12088

Sequence ID dm3.chr3R
Location 25,598,582 – 25,598,725
Length 143
Max. P 0.976887
window16621 window16622

overview

Window 1

Location 25,598,582 – 25,598,686
Length 104
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 97.47
Shannon entropy 0.03465
G+C content 0.57964
Mean single sequence MFE -39.63
Consensus MFE -33.90
Energy contribution -33.90
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.04
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.976887
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25598582 104 + 27905053
GAGAGAGGAGUGGAUAGCGGGAGAGACAGAG--GCAGAGGCAGCGGAAUGGAGCGAGCGGUCGGUCUUUGCCGUCGCCAGUUGCCAGUUGUUCAGUUAUUUUUCGC
((((((.((.((((((((.(......)...(--((((.(((.((((...(((.(((....))).)))...)))).)))..))))).)))))))).)).)))))).. ( -41.00, z-score =  -3.71, R)
>droSim1.chr3R 25270633 106 + 27517382
GAGAGAGUAGCGGAUAGCGGGAGAGACAGAGAGGCAGAGGCAGCGGAAUGGAGCGAGCGGUCGGUCUUUGCCGUCGCCAGUUGCCAGUUGUUCAGUUAUUUUUCGC
((((((.(((((((((((.(......).....(((((.(((.((((...(((.(((....))).)))...)))).)))..))))).))))))).)))))))))).. ( -39.20, z-score =  -2.85, R)
>droSec1.super_4 4449637 104 + 6179234
GAGAGAGGAGCGGAUAGCGGGAGAGACAGAG--GCAGAGGCAGCGGAAUGGAGCGAGCGGUCGGUCUUUGCCGUCGCCAGUUGCCAGUUGUUCAGUUAUUUUUCGC
((((((..((((((((((.(......)...(--((((.(((.((((...(((.(((....))).)))...)))).)))..))))).))))))).))).)))))).. ( -38.70, z-score =  -2.55, R)
>consensus
GAGAGAGGAGCGGAUAGCGGGAGAGACAGAG__GCAGAGGCAGCGGAAUGGAGCGAGCGGUCGGUCUUUGCCGUCGCCAGUUGCCAGUUGUUCAGUUAUUUUUCGC
((((((.....(((((((.((...(((.(.....)...(((.((((...(((.(((....))).)))...)))).))).))).)).))))))).....)))))).. (-33.90 = -33.90 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 25,598,614 – 25,598,725
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 100.00
Shannon entropy -0.00000
G+C content 0.50450
Mean single sequence MFE -38.22
Consensus MFE -38.22
Energy contribution -38.22
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.871153
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25598614 111 + 27905053
CAGAGGCAGCGGAAUGGAGCGAGCGGUCGGUCUUUGCCGUCGCCAGUUGCCAGUUGUUCAGUUAUUUUUCGCUUUUUGUUAAGGCAACUUAUUGAAACGCGACUGCAGCAA
....(((.((((...(((.(((....))).)))...)))).))).(((((.(((((((((((........(((((.....))))).....)))))...))))))))))).. ( -38.22, z-score =  -1.45, R)
>droSim1.chr3R 25270667 111 + 27517382
CAGAGGCAGCGGAAUGGAGCGAGCGGUCGGUCUUUGCCGUCGCCAGUUGCCAGUUGUUCAGUUAUUUUUCGCUUUUUGUUAAGGCAACUUAUUGAAACGCGACUGCAGCAA
....(((.((((...(((.(((....))).)))...)))).))).(((((.(((((((((((........(((((.....))))).....)))))...))))))))))).. ( -38.22, z-score =  -1.45, R)
>droSec1.super_4 4449669 111 + 6179234
CAGAGGCAGCGGAAUGGAGCGAGCGGUCGGUCUUUGCCGUCGCCAGUUGCCAGUUGUUCAGUUAUUUUUCGCUUUUUGUUAAGGCAACUUAUUGAAACGCGACUGCAGCAA
....(((.((((...(((.(((....))).)))...)))).))).(((((.(((((((((((........(((((.....))))).....)))))...))))))))))).. ( -38.22, z-score =  -1.45, R)
>consensus
CAGAGGCAGCGGAAUGGAGCGAGCGGUCGGUCUUUGCCGUCGCCAGUUGCCAGUUGUUCAGUUAUUUUUCGCUUUUUGUUAAGGCAACUUAUUGAAACGCGACUGCAGCAA
....(((.((((...(((.(((....))).)))...)))).))).(((((.(((((((((((........(((((.....))))).....)))))...))))))))))).. (-38.22 = -38.22 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:55:32 2011