Locus 10910

Sequence ID dm3.chr3R
Location 17,422,415 – 17,422,486
Length 71
Max. P 0.993061
window14993 window14994

overview

Window 3

Location 17,422,415 – 17,422,486
Length 71
Sequences 5
Columns 71
Reading direction forward
Mean pairwise identity 99.44
Shannon entropy 0.01017
G+C content 0.41127
Mean single sequence MFE -18.66
Consensus MFE -18.48
Energy contribution -18.68
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.23
SVM RNA-class probability 0.986240
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17422415 71 + 27905053
CGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUUCAAUUUGUAAUUGUAAUUGCAUUUUAUAUACA
.(((.((((((...)))))).)))...((..(((((.((((((.....)))).)).)))))..))...... ( -19.60, z-score =  -2.82, R)
>droEre2.scaffold_4770 13506411 71 - 17746568
CGACCCCGCCGCUACGACGGCGUCAUCUGUUGUGCAUUUCAAUUUGUAAUUGUAAUUGCAUUUUAUAUACA
.((...(((((......)))))...))((..(((((.((((((.....)))).)).)))))..))...... ( -14.90, z-score =  -0.92, R)
>droYak2.chr3R 6260410 71 + 28832112
CGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUUCAAUUUGUAAUUGUAAUUGCAUUUUAUAUACA
.(((.((((((...)))))).)))...((..(((((.((((((.....)))).)).)))))..))...... ( -19.60, z-score =  -2.82, R)
>droSec1.super_6 291521 71 - 4358794
CGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUUCAAUUUGUAAUUGUAAUUGCAUUUUAUAUACA
.(((.((((((...)))))).)))...((..(((((.((((((.....)))).)).)))))..))...... ( -19.60, z-score =  -2.82, R)
>droSim1.chr3R 23471681 71 - 27517382
CGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUUCAAUUUGUAAUUGUAAUUGCAUUUUAUAUACA
.(((.((((((...)))))).)))...((..(((((.((((((.....)))).)).)))))..))...... ( -19.60, z-score =  -2.82, R)
>consensus
CGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUUCAAUUUGUAAUUGUAAUUGCAUUUUAUAUACA
.(((.((((((...)))))).)))...((..(((((.((((((.....)))).)).)))))..))...... (-18.48 = -18.68 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,422,415 – 17,422,486
Length 71
Sequences 5
Columns 71
Reading direction reverse
Mean pairwise identity 99.44
Shannon entropy 0.01017
G+C content 0.41127
Mean single sequence MFE -19.46
Consensus MFE -19.54
Energy contribution -19.38
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -2.70
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.59
SVM RNA-class probability 0.993061
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17422415 71 - 27905053
UGUAUAUAAAAUGCAAUUACAAUUACAAAUUGAAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCG
...........((((.((.((((.....)))))).))))........(((.((((((...)))))).))). ( -19.50, z-score =  -2.80, R)
>droEre2.scaffold_4770 13506411 71 + 17746568
UGUAUAUAAAAUGCAAUUACAAUUACAAAUUGAAAUGCACAACAGAUGACGCCGUCGUAGCGGCGGGGUCG
...........((((.((.((((.....)))))).)))).....(((..((((((....))))))..))). ( -19.30, z-score =  -2.30, R)
>droYak2.chr3R 6260410 71 - 28832112
UGUAUAUAAAAUGCAAUUACAAUUACAAAUUGAAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCG
...........((((.((.((((.....)))))).))))........(((.((((((...)))))).))). ( -19.50, z-score =  -2.80, R)
>droSec1.super_6 291521 71 + 4358794
UGUAUAUAAAAUGCAAUUACAAUUACAAAUUGAAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCG
...........((((.((.((((.....)))))).))))........(((.((((((...)))))).))). ( -19.50, z-score =  -2.80, R)
>droSim1.chr3R 23471681 71 + 27517382
UGUAUAUAAAAUGCAAUUACAAUUACAAAUUGAAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCG
...........((((.((.((((.....)))))).))))........(((.((((((...)))))).))). ( -19.50, z-score =  -2.80, R)
>consensus
UGUAUAUAAAAUGCAAUUACAAUUACAAAUUGAAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCG
...........((((.((.((((.....)))))).))))........(((.((((((...)))))).))). (-19.54 = -19.38 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:32:49 2011