Locus 10333

Sequence ID dm3.chr3R
Location 13,116,488 – 13,116,547
Length 59
Max. P 0.763526
window14206 window14207

overview

Window 6

Location 13,116,488 – 13,116,547
Length 59
Sequences 6
Columns 63
Reading direction forward
Mean pairwise identity 85.75
Shannon entropy 0.26749
G+C content 0.69639
Mean single sequence MFE -27.45
Consensus MFE -21.52
Energy contribution -22.88
Covariance contribution 1.36
Combinations/Pair 1.06
Mean z-score -1.65
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763526
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13116488 59 + 27905053
ACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGCCCGC----
(((....))).....((.(((((..(((((((..........)))))))..))))).))---- ( -29.00, z-score =  -2.10, R)
>droAna3.scaffold_13340 10333071 63 + 23697760
ACCGGAAGGUGCACCGCCGACCAGCAGACGCCAUACUUUGGGUGGUUGCCAUGGCGUCUUGUG
...((..((((...))))..)).(((((((((((......(((....))))))))))).))). ( -23.30, z-score =  -0.70, R)
>droEre2.scaffold_4770 9235465 59 - 17746568
ACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGCCCGC----
(((....))).....((.(((((..(((((((..........)))))))..))))).))---- ( -29.00, z-score =  -2.10, R)
>droYak2.chr3R 17206913 59 + 28832112
ACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGCGGCGGCGUCUUCUGGCCCGC----
(((....))).....((.(((((..(((((((..........)))))))..))))).))---- ( -29.00, z-score =  -1.59, R)
>droSec1.super_12 1093779 59 - 2123299
ACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGACCGC----
.(((((((..((..((((((...))...(((....))).))))))..))))))).....---- ( -25.40, z-score =  -1.33, R)
>droSim1.chr3R 19162218 59 - 27517382
ACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGCCCGC----
(((....))).....((.(((((..(((((((..........)))))))..))))).))---- ( -29.00, z-score =  -2.10, R)
>consensus
ACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGCCCGC____
(((....))).....((.(((((..(((((((..........)))))))..))))).)).... (-21.52 = -22.88 +   1.36)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 13,116,488 – 13,116,547
Length 59
Sequences 6
Columns 63
Reading direction reverse
Mean pairwise identity 85.75
Shannon entropy 0.26749
G+C content 0.69639
Mean single sequence MFE -27.80
Consensus MFE -22.76
Energy contribution -24.02
Covariance contribution 1.25
Combinations/Pair 1.11
Mean z-score -1.21
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.543458
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13116488 59 - 27905053
----GCGGGCCAGAAGACGCCGCCUCGCAAUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGU
----((.(((((..((((((((........))))))))..))))).)).....(((....))) ( -30.40, z-score =  -1.81, R)
>droAna3.scaffold_13340 10333071 63 - 23697760
CACAAGACGCCAUGGCAACCACCCAAAGUAUGGCGUCUGCUGGUCGGCGGUGCACCUUCCGGU
....((((((((((.(...........)))))))))))(((((..((.......))..))))) ( -21.20, z-score =  -0.26, R)
>droEre2.scaffold_4770 9235465 59 + 17746568
----GCGGGCCAGAAGACGCCGCCUCGCAAUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGU
----((.(((((..((((((((........))))))))..))))).)).....(((....))) ( -30.40, z-score =  -1.81, R)
>droYak2.chr3R 17206913 59 - 28832112
----GCGGGCCAGAAGACGCCGCCGCGCAAUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGU
----((.(((((..((((((((........))))))))..))))).)).....(((....))) ( -30.40, z-score =  -1.28, R)
>droSec1.super_12 1093779 59 + 2123299
----GCGGUCCAGAAGACGCCGCCUCGCAAUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGU
----.(((.(((..((((((((........))))))))..)))))).......(((....))) ( -24.00, z-score =  -0.27, R)
>droSim1.chr3R 19162218 59 + 27517382
----GCGGGCCAGAAGACGCCGCCUCGCAAUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGU
----((.(((((..((((((((........))))))))..))))).)).....(((....))) ( -30.40, z-score =  -1.81, R)
>consensus
____GCGGGCCAGAAGACGCCGCCUCGCAAUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGU
....((.(((((..((((((((........))))))))..))))).)).....(((....))) (-22.76 = -24.02 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:21:55 2011