Locus 12420

Sequence ID dm3.chr4
Location 1,016,876 – 1,016,994
Length 118
Max. P 0.994332
window17067 window17068 window17069 window17070

overview

Window 7

Location 1,016,876 – 1,016,992
Length 116
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 92.09
Shannon entropy 0.10895
G+C content 0.33246
Mean single sequence MFE -27.90
Consensus MFE -25.00
Energy contribution -25.00
Covariance contribution 0.00
Combinations/Pair 1.07
Mean z-score -2.37
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967078
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 1016876 116 + 1351857
AGUAGGAAAUACUUUUGGCCUUCAGUAAUUUAAAACG-CUCUAAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUACUGUUCGAAGGCUCGUACGCACAUCCUUUUA-
...((((........(((((((((((((((((.....-...))))).....))))((((((.(((((((.......)))))))))))))...)))))).))........))))....- ( -26.79, z-score =  -2.56, R)
>droSec1.super_40 59901 118 + 298270
AGUAGGAAAUACUUUUGGUCUUCAGUAAUUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUA
...((((....(((..((((((((....)....((((((...((((......))))......(((((((.......)))))))..)))))).)))))))...)))....))))..... ( -28.70, z-score =  -2.46, R)
>droSim1.chr4 786745 118 + 949497
AGUAGGAAAUACUUUUGGUCUUCAGUAACUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUA
...((((....(((..(((((((..........((((((...((((......))))......(((((((.......)))))))..)))))).)))))))...)))....))))..... ( -28.20, z-score =  -2.09, R)
>consensus
AGUAGGAAAUACUUUUGGUCUUCAGUAAUUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUA
...((((....(((..(((((((...................((((......)))).((((.(((((((.......))))))))))).....)))))))...)))....))))..... (-25.00 = -25.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,016,876 – 1,016,992
Length 116
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 92.09
Shannon entropy 0.10895
G+C content 0.33246
Mean single sequence MFE -29.10
Consensus MFE -25.52
Energy contribution -24.97
Covariance contribution -0.55
Combinations/Pair 1.09
Mean z-score -3.25
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.69
SVM RNA-class probability 0.994301
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 1016876 116 - 1351857
-UAAAAGGAUGUGCGUACGAGCCUUCGAACAGUAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUUAGAG-CGUUUUAAAUUACUGAAGGCCAAAAGUAUUUCCUACU
-....((((.((((....(.((((((...((((((..(((((.......)))))...))))))((((....(((......-.)))......)))))))))))....)))).))))... ( -31.50, z-score =  -3.67, R)
>droSec1.super_40 59901 118 - 298270
UAAAAAGGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAAUUACUGAAGACCAAAAGUAUUUCCUACU
.....((((.((((((....(((((((((.(((....(((((.......)))))........((((......))))...))).))).........))))))...)))))).))))... ( -27.70, z-score =  -3.22, R)
>droSim1.chr4 786745 118 - 949497
UAAAAAGGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAGUUACUGAAGACCAAAAGUAUUUCCUACU
.....((((.((((((....((((((.((((((....(((((.......)))))........((((......))))...))).......)))...))))))...)))))).))))... ( -28.11, z-score =  -2.85, R)
>consensus
UAAAAAGGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAAUUACUGAAGACCAAAAGUAUUUCCUACU
.....((((.((((((....((((((...(((.((..(((((.......)))))...)).)))((((.((((.(.....).))))......))))))))))...)))))).))))... (-25.52 = -24.97 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,016,878 – 1,016,994
Length 116
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 91.53
Shannon entropy 0.11673
G+C content 0.34098
Mean single sequence MFE -27.90
Consensus MFE -25.00
Energy contribution -25.00
Covariance contribution 0.00
Combinations/Pair 1.07
Mean z-score -2.39
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.84
SVM RNA-class probability 0.970825
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 1016878 116 + 1351857
UAGGAAAUACUUUUGGCCUUCAGUAAUUUAAAACG-CUCUAAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUACUGUUCGAAGGCUCGUACGCACAUCCUUUUAGG-
.((((........(((((((((((((((((.....-...))))).....))))((((((.(((((((.......)))))))))))))...)))))).))........))))......- ( -26.79, z-score =  -2.59, R)
>droSec1.super_40 59903 118 + 298270
UAGGAAAUACUUUUGGUCUUCAGUAAUUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUAGG
.((((....(((..((((((((....)....((((((...((((......))))......(((((((.......)))))))..)))))).)))))))...)))....))))....... ( -28.70, z-score =  -2.46, R)
>droSim1.chr4 786747 118 + 949497
UAGGAAAUACUUUUGGUCUUCAGUAACUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUAGG
.((((....(((..(((((((..........((((((...((((......))))......(((((((.......)))))))..)))))).)))))))...)))....))))....... ( -28.20, z-score =  -2.12, R)
>consensus
UAGGAAAUACUUUUGGUCUUCAGUAAUUUAAAAUGGCUUAGAGUCAUCAUACUCAGUAUAUGUGUACUAUUUAUGUACAUAAUGCCGUUCGAAGACUUGUAAGCACAUCCUUUUUAGG
.((((....(((..(((((((...................((((......)))).((((.(((((((.......))))))))))).....)))))))...)))....))))....... (-25.00 = -25.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,016,878 – 1,016,994
Length 116
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 91.53
Shannon entropy 0.11673
G+C content 0.34098
Mean single sequence MFE -29.10
Consensus MFE -25.52
Energy contribution -24.97
Covariance contribution -0.55
Combinations/Pair 1.09
Mean z-score -3.22
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.69
SVM RNA-class probability 0.994332
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 1016878 116 - 1351857
-CCUAAAAGGAUGUGCGUACGAGCCUUCGAACAGUAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUUAGAG-CGUUUUAAAUUACUGAAGGCCAAAAGUAUUUCCUA
-......((((.((((....(.((((((...((((((..(((((.......)))))...))))))((((....(((......-.)))......)))))))))))....)))).)))). ( -31.50, z-score =  -3.69, R)
>droSec1.super_40 59903 118 - 298270
CCUAAAAAGGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAAUUACUGAAGACCAAAAGUAUUUCCUA
.......((((.((((((....(((((((((.(((....(((((.......)))))........((((......))))...))).))).........))))))...)))))).)))). ( -27.70, z-score =  -3.17, R)
>droSim1.chr4 786747 118 - 949497
CCUAAAAAGGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAGUUACUGAAGACCAAAAGUAUUUCCUA
.......((((.((((((....((((((.((((((....(((((.......)))))........((((......))))...))).......)))...))))))...)))))).)))). ( -28.11, z-score =  -2.81, R)
>consensus
CCUAAAAAGGAUGUGCUUACAAGUCUUCGAACGGCAUUAUGUACAUAAAUAGUACACAUAUACUGAGUAUGAUGACUCUAAGCCAUUUUAAAUUACUGAAGACCAAAAGUAUUUCCUA
.......((((.((((((....((((((...(((.((..(((((.......)))))...)).)))((((.((((.(.....).))))......))))))))))...)))))).)))). (-25.52 = -24.97 +  -0.55)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:01:49 2011