Locus 7233

Sequence ID dm3.chr3L
Location 13,204,313 – 13,204,388
Length 75
Max. P 0.954383
window9959 window9960

overview

Window 9

Location 13,204,313 – 13,204,388
Length 75
Sequences 14
Columns 75
Reading direction forward
Mean pairwise identity 91.94
Shannon entropy 0.21008
G+C content 0.61006
Mean single sequence MFE -31.61
Consensus MFE -29.26
Energy contribution -29.01
Covariance contribution -0.25
Combinations/Pair 1.41
Mean z-score -1.60
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.32
SVM RNA-class probability 0.925967
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13204313 75 + 24543557
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>droSim1.chr3L 12599696 75 + 22553184
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>droSec1.super_0 5379960 75 + 21120651
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>droYak2.chr3L 13291524 75 + 24197627
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>droEre2.scaffold_4784 13214241 75 + 25762168
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAA
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.63, R)
>droAna3.scaffold_13337 11017576 75 - 23293914
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>dp4.chrXR_group6 7897695 71 - 13314419
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGG----GGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
(((((((..............(((((((.(....).----)))))))(((((.......)))))))))))).... ( -30.60, z-score =  -1.61, R)
>droPer1.super_9196 809 75 + 1238
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>droWil1.scaffold_180698 6735092 75 + 11422946
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>droVir3.scaffold_12970 6178753 75 - 11907090
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>droMoj3.scaffold_6680 9923560 75 - 24764193
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>droGri2.scaffold_15110 23222284 75 + 24565398
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -32.40, z-score =  -1.73, R)
>anoGam1.chr3L 28727336 75 - 41284009
GGCUCAAUGGUCUAGGGGUAUGAUUUUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGUUGAGCCCGAU
((((((((.......(((.....(((((((.......)))))))..)))(((.......))).)))))))).... ( -29.10, z-score =  -1.26, R)
>triCas2.ChLG5 14942443 70 + 18847211
GGCCUCGUGGCCUAGUGGUAUAAGCGCCACUUACGACGCGGGAGGUCGAGGGUUCGAACCCGGAUCAGGU-----
...((((((....((((((......)))))).....)))))).((((..((((....)))).))))....----- ( -26.50, z-score =  -0.60, R)
>consensus
GGCUCGUUGGUCUAGGGGUAUGAUUUCCGCUUAGGGUGCGGGAGGUCCCGGGUUCAAAUCCCGGACGAGCCCAAG
((((((((......((((.....(((((((.......))))))).))))(((.......))).)))))))).... (-29.26 = -29.01 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 13,204,313 – 13,204,388
Length 75
Sequences 14
Columns 75
Reading direction reverse
Mean pairwise identity 91.94
Shannon entropy 0.21008
G+C content 0.61006
Mean single sequence MFE -25.56
Consensus MFE -23.51
Energy contribution -23.52
Covariance contribution 0.01
Combinations/Pair 1.38
Mean z-score -1.84
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.60
SVM RNA-class probability 0.954383
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13204313 75 - 24543557
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>droSim1.chr3L 12599696 75 - 22553184
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>droSec1.super_0 5379960 75 - 21120651
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>droYak2.chr3L 13291524 75 - 24197627
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>droEre2.scaffold_4784 13214241 75 - 25762168
UUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.93, R)
>droAna3.scaffold_13337 11017576 75 + 23293914
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>dp4.chrXR_group6 7897695 71 + 13314419
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCC----CCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))((..(((----........)))..))..............))))))) ( -22.70, z-score =  -0.97, R)
>droPer1.super_9196 809 75 - 1238
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>droWil1.scaffold_180698 6735092 75 - 11422946
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>droVir3.scaffold_12970 6178753 75 + 11907090
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>droMoj3.scaffold_6680 9923560 75 + 24764193
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>droGri2.scaffold_15110 23222284 75 - 24565398
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -26.10, z-score =  -1.94, R)
>anoGam1.chr3L 28727336 75 + 41284009
AUCGGGCUCAACCGGGAUUUGAACCCGGGACCUCUCGCACCCGAAGCGAAAAUCAUACCCCUAGACCAUUGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) ( -23.40, z-score =  -1.91, R)
>triCas2.ChLG5 14942443 70 - 18847211
-----ACCUGAUCCGGGUUCGAACCCUCGACCUCCCGCGUCGUAAGUGGCGCUUAUACCACUAGGCCACGAGGCC
-----....(((.((((.((((....))))...)))).)))...(((((........))))).((((....)))) ( -24.60, z-score =  -1.54, R)
>consensus
CUUGGGCUCGUCCGGGAUUUGAACCCGGGACCUCCCGCACCCUAAGCGGAAAUCAUACCCCUAGACCAACGAGCC
....((((((((((((.......)))))......((((.......))))...................))))))) (-23.51 = -23.52 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:23:02 2011