Locus 2788

Sequence ID dm3.chr2L
Location 22,393,015 – 22,393,074
Length 59
Max. P 0.997681
window3834 window3835

overview

Window 4

Location 22,393,015 – 22,393,074
Length 59
Sequences 5
Columns 59
Reading direction forward
Mean pairwise identity 84.24
Shannon entropy 0.28441
G+C content 0.64317
Mean single sequence MFE -22.68
Consensus MFE -15.58
Energy contribution -17.62
Covariance contribution 2.04
Combinations/Pair 1.05
Mean z-score -1.77
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.648243
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22393015 59 + 23011544
GGCCGGCGGUAGUGCUCUACUGACUGGGGUCUCGGAGCUCUACUCACUCCACCACCGCC
....((((((.(((......(((.((((((......)))))).)))...))).)))))) ( -20.30, z-score =  -0.34, R)
>droEre2.scaffold_4929 12726921 59 - 26641161
GGCCGGCGGUAGCACUCUCCUAACUGGGGAGACCGAGCUCUACUCACUCCACUACCGCC
....((((((((..((((((.....))))))...(((.....)))......)))))))) ( -26.00, z-score =  -3.60, R)
>droYak2.chr2L 7924854 53 + 22324452
GGCCGGCGUCAGUUCUCUCC-GACAAGGAUGUCGAAGCU-----GACUCCACUACCGCC
....((.(((((((.....(-((((....))))).))))-----))).))......... ( -16.30, z-score =  -0.91, R)
>droSec1.super_162 6877 59 + 37850
GGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCC
....((((((((((......(((.((((((......)))))).)))...)))))))))) ( -25.40, z-score =  -2.00, R)
>droSim1.chrU 11708030 59 + 15797150
GGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCC
....((((((((((......(((.((((((......)))))).)))...)))))))))) ( -25.40, z-score =  -2.00, R)
>consensus
GGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCC
....(((((((((((((((.....))))))...((((.........))))))))))))) (-15.58 = -17.62 +   2.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 22,393,015 – 22,393,074
Length 59
Sequences 5
Columns 59
Reading direction reverse
Mean pairwise identity 84.24
Shannon entropy 0.28441
G+C content 0.64317
Mean single sequence MFE -26.16
Consensus MFE -22.24
Energy contribution -22.24
Covariance contribution 0.00
Combinations/Pair 1.29
Mean z-score -3.17
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.15
SVM RNA-class probability 0.997681
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22393015 59 - 23011544
GGCGGUGGUGGAGUGAGUAGAGCUCCGAGACCCCAGUCAGUAGAGCACUACCGCCGGCC
((((((((((((((.......)))))..(((....)))........))))))))).... ( -26.30, z-score =  -2.94, R)
>droEre2.scaffold_4929 12726921 59 + 26641161
GGCGGUAGUGGAGUGAGUAGAGCUCGGUCUCCCCAGUUAGGAGAGUGCUACCGCCGGCC
(((((((((.((((.......))))(.(((((.......))))).)))))))))).... ( -27.80, z-score =  -3.15, R)
>droYak2.chr2L 7924854 53 - 22324452
GGCGGUAGUGGAGUC-----AGCUUCGACAUCCUUGUC-GGAGAGAACUGACGCCGGCC
...(((...((.(((-----((((((((((....))))-))))....))))).)).))) ( -21.90, z-score =  -1.91, R)
>droSec1.super_162 6877 59 - 37850
GGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCC
((((((((((((((.......)))))(((......)))........))))))))).... ( -27.40, z-score =  -3.94, R)
>droSim1.chrU 11708030 59 - 15797150
GGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCC
((((((((((((((.......)))))(((......)))........))))))))).... ( -27.40, z-score =  -3.94, R)
>consensus
GGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCC
((((((((((((((.......)))))(((......)))........))))))))).... (-22.24 = -22.24 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:57:55 2011