Locus 804

Sequence ID dm3.chr2L
Location 5,757,204 – 5,757,307
Length 103
Max. P 0.871847
window1085 window1086

overview

Window 5

Location 5,757,204 – 5,757,304
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 83.22
Shannon entropy 0.28711
G+C content 0.47524
Mean single sequence MFE -27.90
Consensus MFE -22.70
Energy contribution -23.14
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.47
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.772117
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5757204 100 + 23011544
AUUCCUGGUACGAAUUCAAUUGCACUUGCAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGUCCGAA-GGACCCUUUUUCGCGGCCAUGCACAUGA
....((..(((((((((...(((....)))..(((((....)))))))))).))))..))...(((((((((-(((...))))))).)))))......... ( -28.10, z-score =  -0.98, R)
>droEre2.scaffold_4929 5849274 101 + 26641161
AUCCUAGGUACGUAUUCCAUUGCACUUGCAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGCCCAAAAGGACCCUUUUUCGCGGCCAUGCACAUGA
......((........))..(((....)))(((((((....))))))).((((((((......(((((((((((....)))))..).))))).)))))))) ( -28.50, z-score =  -0.78, R)
>droYak2.chr2L 8890335 101 - 22324452
AUUCUCGGUACGAAUUCAAUUGCACUCGUAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGCCCAAAGGACCCCUUUUUCGCGGCCACGCACAUGA
.(((..(((((((............)))))))(((((....))))))))((((((((((((..(((...(((((...))))).)))..)))).)))))))) ( -27.50, z-score =  -0.82, R)
>droSec1.super_5 3836028 82 + 5866729
------------------AUUCCACUUGCAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGCCCGAA-GGACCCUUUUUCGCGGCCAUGCACAUGA
------------------............(((((((....))))))).((((((((......(((((((((-(((...))))))).))))).)))))))) ( -28.50, z-score =  -2.69, R)
>droSim1.chr2L 5553840 82 + 22036055
------------------AUUCCACUUGCAUUGCCUACUUAUGGGCGAAUAAUGUGUUGGUUUUGGCCCGAA-GGACCCUUUUUCGCGGCCAUGCACAUGA
------------------............(((((((....)))))))...((((((......(((((((((-(((...))))))).))))).)))))).. ( -26.90, z-score =  -2.06, R)
>consensus
AU_C__GGUACG_AUUC_AUUGCACUUGCAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGCCCGAA_GGACCCUUUUUCGCGGCCAUGCACAUGA
..............................(((((((....))))))).((((((((......(((((((((.(....)...)))).))))).)))))))) (-22.70 = -23.14 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,757,207 – 5,757,307
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 83.42
Shannon entropy 0.28166
G+C content 0.47326
Mean single sequence MFE -28.40
Consensus MFE -23.50
Energy contribution -23.94
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.62
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.871847
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5757207 100 + 23011544
CCUGGUACGAAUUCAAUUGCACUUGCAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGUCCGAA-GGACCCUUUUUCGCGGCCAUGCACAUGAAAU
.................(((....)))(((((((....))))))).((((((((......(((((((((-(((...))))))).))))).))))))))... ( -28.60, z-score =  -1.13, R)
>droEre2.scaffold_4929 5849277 101 + 26641161
CUAGGUACGUAUUCCAUUGCACUUGCAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGCCCAAAAGGACCCUUUUUCGCGGCCAUGCACAUGAAAU
...((........))..(((....)))(((((((....))))))).((((((((......(((((((((((....)))))..).))))).))))))))... ( -29.30, z-score =  -1.10, R)
>droYak2.chr2L 8890338 101 - 22324452
CUCGGUACGAAUUCAAUUGCACUCGUAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGCCCAAAGGACCCCUUUUUCGCGGCCACGCACAUGAAAU
.(((((((((............)))))))(((((....))))))).((((((((((((..(((...(((((...))))).)))..)))).))))))))... ( -27.90, z-score =  -0.94, R)
>droSec1.super_5 3836031 82 + 5866729
------------------CCACUUGCAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGCCCGAA-GGACCCUUUUUCGCGGCCAUGCACAUGAAAU
------------------.........(((((((....))))))).((((((((......(((((((((-(((...))))))).))))).))))))))... ( -29.30, z-score =  -2.89, R)
>droSim1.chr2L 5553843 82 + 22036055
------------------CCACUUGCAUUGCCUACUUAUGGGCGAAUAAUGUGUUGGUUUUGGCCCGAA-GGACCCUUUUUCGCGGCCAUGCACAUGAAAU
------------------.........(((((((....)))))))...((((((......(((((((((-(((...))))))).))))).))))))..... ( -26.90, z-score =  -2.05, R)
>consensus
C__GGUACG_AUUC_AUUGCACUUGCAUUGCCUACUUAUGGGCGAAUUAUGUGUUGGUUUUGGCCCGAA_GGACCCUUUUUCGCGGCCAUGCACAUGAAAU
...........................(((((((....))))))).((((((((......(((((((((.(....)...)))).))))).))))))))... (-23.50 = -23.94 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:19:47 2011