Locus 12840

Sequence ID dm3.chrX
Location 2,580,801 – 2,580,895
Length 94
Max. P 0.970000
window17650 window17651

overview

Window 0

Location 2,580,801 – 2,580,895
Length 94
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 96.45
Shannon entropy 0.04885
G+C content 0.48582
Mean single sequence MFE -29.70
Consensus MFE -27.23
Energy contribution -27.68
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.62
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.731874
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2580801 94 + 22422827
CUGCGUCAAAGUUCACCCACAUAUGGGAUGCGAACUGGGUUAACCAGCGAGUUACACAAUCCUUGGUGGGUAUAAACUGAAGGAUUUGGGCAGA
(((((((..((((.((((((....(((((((...((((.....))))...))......)))))..))))))...))))....)))....)))). ( -28.60, z-score =  -1.44, R)
>droSim1.chrX_random 1344103 94 + 5698898
CUGCGUCAAAGUUCACCCACAUAUGGGAUGCGAACUGGGUUAACCACCGAGUUACACAAUCCUUGGUGGGGAUAAACUGGAAGAUUUGGGCAGA
((((.(((((.(((((((((....(((((...((((.(((.....))).)))).....)))))..))))).......))))...))))))))). ( -31.91, z-score =  -2.24, R)
>droSec1.super_10 2342464 94 + 3036183
CUGCGUCAAAGUUCACCCACAUAUGGGAUGCGAACUGGGUUAACCACCGAGUUACACAAUCCUUGGUGGGGAUAAACUGGAGGAUUUGGACAGA
....(((.((((((.(((((....(((((...((((.(((.....))).)))).....)))))..)))))(.....)....)))))).)))... ( -28.60, z-score =  -1.19, R)
>consensus
CUGCGUCAAAGUUCACCCACAUAUGGGAUGCGAACUGGGUUAACCACCGAGUUACACAAUCCUUGGUGGGGAUAAACUGGAGGAUUUGGGCAGA
((((.(((((.(((((((((....(((((...((((.(((.....))).)))).....)))))..))))).......))))...))))))))). (-27.23 = -27.68 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 2,580,801 – 2,580,895
Length 94
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 96.45
Shannon entropy 0.04885
G+C content 0.48582
Mean single sequence MFE -26.68
Consensus MFE -25.40
Energy contribution -25.51
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.28
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.82
SVM RNA-class probability 0.970000
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2580801 94 - 22422827
UCUGCCCAAAUCCUUCAGUUUAUACCCACCAAGGAUUGUGUAACUCGCUGGUUAACCCAGUUCGCAUCCCAUAUGUGGGUGAACUUUGACGCAG
.((((.(((.......(((((..((((((...((..((((......(((((.....))))).))))..))....))))))))))))))..)))) ( -25.31, z-score =  -2.17, R)
>droSim1.chrX_random 1344103 94 - 5698898
UCUGCCCAAAUCUUCCAGUUUAUCCCCACCAAGGAUUGUGUAACUCGGUGGUUAACCCAGUUCGCAUCCCAUAUGUGGGUGAACUUUGACGCAG
.((((.(((.......(((((((((.((....((((.(((.((((.(((.....))).)))))))))))....)).))))))))))))..)))) ( -28.21, z-score =  -2.62, R)
>droSec1.super_10 2342464 94 - 3036183
UCUGUCCAAAUCCUCCAGUUUAUCCCCACCAAGGAUUGUGUAACUCGGUGGUUAACCCAGUUCGCAUCCCAUAUGUGGGUGAACUUUGACGCAG
.((((.(((.......(((((((((.((....((((.(((.((((.(((.....))).)))))))))))....)).))))))))))))..)))) ( -26.51, z-score =  -2.06, R)
>consensus
UCUGCCCAAAUCCUCCAGUUUAUCCCCACCAAGGAUUGUGUAACUCGGUGGUUAACCCAGUUCGCAUCCCAUAUGUGGGUGAACUUUGACGCAG
.((((.(((.......((((((..(((((...((..((((.((((.(((.....))).))))))))..))....))))))))))))))..)))) (-25.40 = -25.51 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:09:46 2011