Locus 1785

Sequence ID dm3.chr2L
Location 13,771,113 – 13,771,207
Length 94
Max. P 0.995639
window2458 window2459

overview

Window 8

Location 13,771,113 – 13,771,207
Length 94
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 94.56
Shannon entropy 0.09348
G+C content 0.41976
Mean single sequence MFE -25.92
Consensus MFE -20.76
Energy contribution -20.96
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.87
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956807
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13771113 94 + 23011544
GAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACAAAAUAUAUAGUUUCUAGCGGAAUUUCUGCCAACAAAAGGGGUC----CAGUGG
.........(((((((..(..(((((((((((...(((((.......))))))))))))).)))...)..))))........((...)----)..))) ( -23.50, z-score =  -2.69, R)
>droEre2.scaffold_4929 14946049 98 - 26641161
GAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAAUAUAUAUACAAAAUAUAUAGUUUCUAGCGGAAUUGCUGCCAAAACAAGGGGUCGUGCCAGUGG
......(((.((((((.....(((((((((((...(((((.......))))))))))))).)))...)))))).)))..((..((......))..)). ( -26.30, z-score =  -2.49, R)
>droYak2.chr2L 10182876 94 + 22324452
GAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACCAAAUAUAUAGUUUCUUGCGGACUUGCUGCCAAAACAAGGGGUC----CAGUGG
......(((.(((((((....(((((((((((...(((((.......)))))))))))).))))..))))))).)))..((..(....----)..)). ( -27.40, z-score =  -2.81, R)
>droSec1.super_3 36954 94 + 7220098
GAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACAAAAUAUAUAGUUUCUAGCGUAAUUGCUGCCAACACAAGGGGUC----CAGUGG
......(((.((((((....((((((((((((...(((((.......))))))))))))).))))..)))))).)))(((...(....----).))). ( -26.20, z-score =  -3.19, R)
>droSim1.chr2L 13530333 94 + 22036055
GAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACAAAAUAUAUAGUUUCUAGCGUAAUUGCUGCCAACACAAGGGGUC----CAGUGG
......(((.((((((....((((((((((((...(((((.......))))))))))))).))))..)))))).)))(((...(....----).))). ( -26.20, z-score =  -3.19, R)
>consensus
GAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACAAAAUAUAUAGUUUCUAGCGGAAUUGCUGCCAACACAAGGGGUC____CAGUGG
......(((.((((((.....(((((((((((...(((((.......))))))))))))).)))...)))))).)))..................... (-20.76 = -20.96 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,771,113 – 13,771,207
Length 94
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 94.56
Shannon entropy 0.09348
G+C content 0.41976
Mean single sequence MFE -26.49
Consensus MFE -23.48
Energy contribution -24.08
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -3.41
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.83
SVM RNA-class probability 0.995639
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13771113 94 - 23011544
CCACUG----GACCCCUUUUGUUGGCAGAAAUUCCGCUAGAAACUAUAUAUUUUGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUC
......----........((((..((((......(((.(((((((((((..............)))))))))))))).....))))..))))...... ( -26.94, z-score =  -4.38, R)
>droEre2.scaffold_4929 14946049 98 + 26641161
CCACUGGCACGACCCCUUGUUUUGGCAGCAAUUCCGCUAGAAACUAUAUAUUUUGUAUAUAUAUUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUC
..................(..(((.(((((....(((.(((((((((((((.........))).)))))))))))))......))))).)))..)... ( -24.30, z-score =  -2.52, R)
>droYak2.chr2L 10182876 94 - 22324452
CCACUG----GACCCCUUGUUUUGGCAGCAAGUCCGCAAGAAACUAUAUAUUUGGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUC
......----........(..(((.(((((((..((((.((((((((((..............)))))))))))))).))...))))).)))..)... ( -25.34, z-score =  -2.31, R)
>droSec1.super_3 36954 94 - 7220098
CCACUG----GACCCCUUGUGUUGGCAGCAAUUACGCUAGAAACUAUAUAUUUUGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUC
......----.........(((..((((.....((((.(((((((((((..............)))))))))))))))....))))..)))....... ( -27.94, z-score =  -3.93, R)
>droSim1.chr2L 13530333 94 - 22036055
CCACUG----GACCCCUUGUGUUGGCAGCAAUUACGCUAGAAACUAUAUAUUUUGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUC
......----.........(((..((((.....((((.(((((((((((..............)))))))))))))))....))))..)))....... ( -27.94, z-score =  -3.93, R)
>consensus
CCACUG____GACCCCUUGUGUUGGCAGCAAUUCCGCUAGAAACUAUAUAUUUUGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUC
...................(((..((((......(((.(((((((((((..............)))))))))))))).....))))..)))....... (-23.48 = -24.08 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:38:48 2011