Locus 10003

Sequence ID dm3.chr3R
Location 10,482,787 – 10,482,863
Length 76
Max. P 0.995108
window13748 window13749

overview

Window 8

Location 10,482,787 – 10,482,863
Length 76
Sequences 3
Columns 87
Reading direction forward
Mean pairwise identity 77.20
Shannon entropy 0.30321
G+C content 0.43618
Mean single sequence MFE -21.93
Consensus MFE -19.90
Energy contribution -20.68
Covariance contribution 0.78
Combinations/Pair 1.13
Mean z-score -2.56
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.77
SVM RNA-class probability 0.995108
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10482787 76 + 27905053
CGGUCAUGGUUAAUUCACACCACAA-----------CUAAACGCCGAGAUGCCGAACAUAUGAGAGGCUCGACUUAAGAUGUUCGGC
((((..(((((............))-----------)))...))))....(((((((((....(((......)))...))))))))) ( -20.60, z-score =  -1.93, R)
>droSec1.super_0 9566333 76 - 21120651
CAGUCUUGGUUCAUAGAUACCAUAU-----------AUAAACGCUGAGAUGCUGAAUAUCUAAGAGGCUCGACUUUAGAUGUUCGGC
..((((..((......(((...)))-----------......))..))))((((((((((((.(((......))))))))))))))) ( -22.30, z-score =  -2.59, R)
>droSim1.chr3R 16537479 87 - 27517382
CUGUCUUUGUUCAUAGAUACCAUAUUCAUACCACAAAUAAACGCUGAGAUGCCGAACAUCUAACAGGCUCGACUUUAGAUGUUCGGC
.(((((........)))))...............................(((((((((((((.((......))))))))))))))) ( -22.90, z-score =  -3.15, R)
>consensus
CAGUCUUGGUUCAUAGAUACCAUAU___________AUAAACGCUGAGAUGCCGAACAUCUAAGAGGCUCGACUUUAGAUGUUCGGC
..((((((((................................))))))))(((((((((((((.((......))))))))))))))) (-19.90 = -20.68 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 10,482,787 – 10,482,863
Length 76
Sequences 3
Columns 87
Reading direction reverse
Mean pairwise identity 77.20
Shannon entropy 0.30321
G+C content 0.43618
Mean single sequence MFE -20.63
Consensus MFE -15.27
Energy contribution -16.93
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.851048
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10482787 76 - 27905053
GCCGAACAUCUUAAGUCGAGCCUCUCAUAUGUUCGGCAUCUCGGCGUUUAG-----------UUGUGGUGUGAAUUAACCAUGACCG
(((((((((....((........))...))))))))).............(-----------(..((((........))))..)).. ( -22.50, z-score =  -2.15, R)
>droSec1.super_0 9566333 76 + 21120651
GCCGAACAUCUAAAGUCGAGCCUCUUAGAUAUUCAGCAUCUCAGCGUUUAU-----------AUAUGGUAUCUAUGAACCAAGACUG
((.(((.((((((((......)).)))))).))).))......(.((((((-----------(.........))))))))....... ( -12.00, z-score =  -0.02, R)
>droSim1.chr3R 16537479 87 + 27517382
GCCGAACAUCUAAAGUCGAGCCUGUUAGAUGUUCGGCAUCUCAGCGUUUAUUUGUGGUAUGAAUAUGGUAUCUAUGAACAAAGACAG
(((((((((((((((......)).)))))))))))))........((((((..(((.(((....))).)))..))))))........ ( -27.40, z-score =  -3.28, R)
>consensus
GCCGAACAUCUAAAGUCGAGCCUCUUAGAUGUUCGGCAUCUCAGCGUUUAU___________AUAUGGUAUCUAUGAACCAAGACAG
(((((((((((((((......)).)))))))))))))............................((((........))))...... (-15.27 = -16.93 +   1.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:15:33 2011