Locus 11060

Sequence ID dm3.chr3R
Location 18,388,447 – 18,388,537
Length 90
Max. P 0.980773
window15192 window15193

overview

Window 2

Location 18,388,447 – 18,388,537
Length 90
Sequences 3
Columns 90
Reading direction forward
Mean pairwise identity 99.26
Shannon entropy 0.01020
G+C content 0.37778
Mean single sequence MFE -21.70
Consensus MFE -21.17
Energy contribution -21.50
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.06
SVM RNA-class probability 0.980773
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18388447 90 + 27905053
AGCUUUAGUUUUUGUUUAGCCGAACUUUUGUCUCGGCUAUUUGGCAUCUUGCUCAUCCUCAUCUUUGACUUUAGCUUUAGCUUUAAGAUG
((((..((((...((((((((((((....)).)))))))...(((.....))).............)))...))))..))))........ ( -21.10, z-score =  -2.18, R)
>droSim1.chr3R 18198148 90 + 27517382
AGCUUUAGUUUUUGUUUAGCCGAACUUUUGUCUCGGCUAUUUGGCAUCUUGCUCAUCCUCAUCUUUGACUUUAGCUAUAGCUUUAAGAUG
((((.(((((...((((((((((((....)).)))))))...(((.....))).............)))...))))).))))........ ( -22.00, z-score =  -2.46, R)
>droSec1.super_0 18741590 90 + 21120651
AGCUUUAGUUUUUGUUUAGCCGAACUUUUGUCUCGGCUAUUUGGCAUCUUGCUCAUCCUCAUCUUUGACUUUAGCUAUAGCUUUAAGAUG
((((.(((((...((((((((((((....)).)))))))...(((.....))).............)))...))))).))))........ ( -22.00, z-score =  -2.46, R)
>consensus
AGCUUUAGUUUUUGUUUAGCCGAACUUUUGUCUCGGCUAUUUGGCAUCUUGCUCAUCCUCAUCUUUGACUUUAGCUAUAGCUUUAAGAUG
((((.(((((...((((((((((((....)).)))))))...(((.....))).............)))...))))).))))........ (-21.17 = -21.50 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,388,447 – 18,388,537
Length 90
Sequences 3
Columns 90
Reading direction reverse
Mean pairwise identity 99.26
Shannon entropy 0.01020
G+C content 0.37778
Mean single sequence MFE -18.30
Consensus MFE -18.30
Energy contribution -18.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.936387
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18388447 90 - 27905053
CAUCUUAAAGCUAAAGCUAAAGUCAAAGAUGAGGAUGAGCAAGAUGCCAAAUAGCCGAGACAAAAGUUCGGCUAAACAAAAACUAAAGCU
........((((...(((...(((.........))).)))...........((((((((.(....)))))))))............)))) ( -18.30, z-score =  -1.75, R)
>droSim1.chr3R 18198148 90 - 27517382
CAUCUUAAAGCUAUAGCUAAAGUCAAAGAUGAGGAUGAGCAAGAUGCCAAAUAGCCGAGACAAAAGUUCGGCUAAACAAAAACUAAAGCU
........((((...(((...(((.........))).)))...........((((((((.(....)))))))))............)))) ( -18.30, z-score =  -1.68, R)
>droSec1.super_0 18741590 90 - 21120651
CAUCUUAAAGCUAUAGCUAAAGUCAAAGAUGAGGAUGAGCAAGAUGCCAAAUAGCCGAGACAAAAGUUCGGCUAAACAAAAACUAAAGCU
........((((...(((...(((.........))).)))...........((((((((.(....)))))))))............)))) ( -18.30, z-score =  -1.68, R)
>consensus
CAUCUUAAAGCUAUAGCUAAAGUCAAAGAUGAGGAUGAGCAAGAUGCCAAAUAGCCGAGACAAAAGUUCGGCUAAACAAAAACUAAAGCU
........((((...(((...(((.........))).)))...........((((((((.(....)))))))))............)))) (-18.30 = -18.30 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:35:35 2011