Locus 8836

Sequence ID dm3.chr3R
Location 1,978,596 – 1,978,649
Length 53
Max. P 0.796195
window12129 window12130

overview

Window 9

Location 1,978,596 – 1,978,649
Length 53
Sequences 6
Columns 53
Reading direction forward
Mean pairwise identity 97.11
Shannon entropy 0.05412
G+C content 0.36164
Mean single sequence MFE -6.13
Consensus MFE -5.85
Energy contribution -6.02
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.20
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.592932
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1978596 53 + 27905053
UUGUCAACGAUAAACGACAAAAGCGAGAAAAAUAUUUCACGACAAAACUGAGG
(((((..((.....))......(.((((......)))).))))))........ (  -6.30, z-score =  -1.22, R)
>droAna3.scaffold_13340 5536492 53 - 23697760
UUGUCAACGAUAAACGACAAAAGCGAGAAAAAUAUUUCACGACACAGCCGAAG
(((((..........)))))..(((.((((....)))).)).).......... (  -5.30, z-score =  -0.80, R)
>droEre2.scaffold_4770 2237491 53 + 17746568
UUGUCAACGAUAAACGACAAAAGCGAGAAAAAUAUUUCACGACAAAACUGAAG
(((((..((.....))......(.((((......)))).))))))........ (  -6.30, z-score =  -1.51, R)
>droYak2.chr3R 17921811 53 + 28832112
UUGUCAACGAUAAACGACAAAAGCGAGAAAAAUAUUUCACGACAAAACUGAGG
(((((..((.....))......(.((((......)))).))))))........ (  -6.30, z-score =  -1.22, R)
>droSec1.super_6 2079139 53 + 4358794
UUGUCAACGAUAAACGACAAAAGCGAGAAAAAUAUUUCACGACAAAACUGAGG
(((((..((.....))......(.((((......)))).))))))........ (  -6.30, z-score =  -1.22, R)
>droSim1.chr3R 2008674 53 + 27517382
UUGUCAACGAUAAACGACAAAAGCGAGAAAAAUAUUUCACGACAAAACUGAGG
(((((..((.....))......(.((((......)))).))))))........ (  -6.30, z-score =  -1.22, R)
>consensus
UUGUCAACGAUAAACGACAAAAGCGAGAAAAAUAUUUCACGACAAAACUGAGG
(((((..((.....))......(.((((......)))).))))))........ ( -5.85 =  -6.02 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 1,978,596 – 1,978,649
Length 53
Sequences 6
Columns 53
Reading direction reverse
Mean pairwise identity 97.11
Shannon entropy 0.05412
G+C content 0.36164
Mean single sequence MFE -7.47
Consensus MFE -7.40
Energy contribution -7.40
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.21
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.796195
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1978596 53 - 27905053
CCUCAGUUUUGUCGUGAAAUAUUUUUCUCGCUUUUGUCGUUUAUCGUUGACAA
..........(.((.((((....)))).)))..((((((........)))))) (  -7.40, z-score =  -1.36, R)
>droAna3.scaffold_13340 5536492 53 + 23697760
CUUCGGCUGUGUCGUGAAAUAUUUUUCUCGCUUUUGUCGUUUAUCGUUGACAA
...((((...(.((.((((....)))).)))....)))).............. (  -7.80, z-score =  -0.59, R)
>droEre2.scaffold_4770 2237491 53 - 17746568
CUUCAGUUUUGUCGUGAAAUAUUUUUCUCGCUUUUGUCGUUUAUCGUUGACAA
..........(.((.((((....)))).)))..((((((........)))))) (  -7.40, z-score =  -1.22, R)
>droYak2.chr3R 17921811 53 - 28832112
CCUCAGUUUUGUCGUGAAAUAUUUUUCUCGCUUUUGUCGUUUAUCGUUGACAA
..........(.((.((((....)))).)))..((((((........)))))) (  -7.40, z-score =  -1.36, R)
>droSec1.super_6 2079139 53 - 4358794
CCUCAGUUUUGUCGUGAAAUAUUUUUCUCGCUUUUGUCGUUUAUCGUUGACAA
..........(.((.((((....)))).)))..((((((........)))))) (  -7.40, z-score =  -1.36, R)
>droSim1.chr3R 2008674 53 - 27517382
CCUCAGUUUUGUCGUGAAAUAUUUUUCUCGCUUUUGUCGUUUAUCGUUGACAA
..........(.((.((((....)))).)))..((((((........)))))) (  -7.40, z-score =  -1.36, R)
>consensus
CCUCAGUUUUGUCGUGAAAUAUUUUUCUCGCUUUUGUCGUUUAUCGUUGACAA
..........(.((.((((....)))).)))..((((((........)))))) ( -7.40 =  -7.40 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:53:05 2011