Locus 4528

Sequence ID dm3.chr2R
Location 13,783,501 – 13,783,552
Length 51
Max. P 0.990323
window6202 window6203

overview

Window 2

Location 13,783,501 – 13,783,552
Length 51
Sequences 8
Columns 51
Reading direction forward
Mean pairwise identity 97.48
Shannon entropy 0.05069
G+C content 0.42157
Mean single sequence MFE -11.44
Consensus MFE -11.35
Energy contribution -11.24
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.47
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.41
SVM RNA-class probability 0.990323
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13783501 51 + 21146708
GGAAUUAAAAAUUCCAAACUCGUUUCGCCCUCUUACAAGGCGAUUUCGUCU
(((((.....))))).....((..(((((.........)))))...))... ( -11.70, z-score =  -2.79, R)
>droSim1.chr2R 12525825 51 + 19596830
GGAAUUAAAAAUUCCAGACUCGUUUCGCCCUCUUACAAGGCGAUUUCGCCU
(((((.....)))))......................(((((....))))) ( -11.60, z-score =  -1.86, R)
>droSec1.super_1 11278715 51 + 14215200
GGAAUUAAAAAUUCCAAACUCGUUUCGCCCUCUUACAAGGCGAUUUCGCCU
(((((.....)))))......................(((((....))))) ( -11.60, z-score =  -2.52, R)
>droYak2.chr2R 5739659 51 - 21139217
GGAAUUAAAAAUUCCAAACUCGUUUCGCCCUCUUACAAGGCGAUUUCGCCU
(((((.....)))))......................(((((....))))) ( -11.60, z-score =  -2.52, R)
>droEre2.scaffold_4845 8010806 51 + 22589142
GGAAUUAAAAAUUCCAAACUCGUUUCGCCCUCUUACAAGGCGAUUUCGCCU
(((((.....)))))......................(((((....))))) ( -11.60, z-score =  -2.52, R)
>droAna3.scaffold_13266 9477054 51 - 19884421
GGAAUUAAAAAUUCCAAACUCGUUUCGUCCUCUUACAAGGCGAUUUCGCUU
(((((.....))))).....((..(((.(((......))))))...))... ( -10.00, z-score =  -2.00, R)
>dp4.chr3 6242830 51 + 19779522
GGAAUUAAAAAUUCCAAACUCGUUUCGCCCUCUUACAAGGCGAUUUCGUCU
(((((.....))))).....((..(((((.........)))))...))... ( -11.70, z-score =  -2.79, R)
>droPer1.super_2 6457531 51 + 9036312
GGAAUUAAAAAUUCCAAACUCGUUUCGCCCUCUUACAAGGCGAUUUCGUCU
(((((.....))))).....((..(((((.........)))))...))... ( -11.70, z-score =  -2.79, R)
>consensus
GGAAUUAAAAAUUCCAAACUCGUUUCGCCCUCUUACAAGGCGAUUUCGCCU
(((((.....))))).....((..(((((.........)))))...))... (-11.35 = -11.24 +  -0.11)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 13,783,501 – 13,783,552
Length 51
Sequences 8
Columns 51
Reading direction reverse
Mean pairwise identity 97.48
Shannon entropy 0.05069
G+C content 0.42157
Mean single sequence MFE -13.18
Consensus MFE -13.04
Energy contribution -12.71
Covariance contribution -0.33
Combinations/Pair 1.19
Mean z-score -1.57
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.26
SVM RNA-class probability 0.917431
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13783501 51 - 21146708
AGACGAAAUCGCCUUGUAAGAGGGCGAAACGAGUUUGGAAUUUUUAAUUCC
((((....(((((((.....))))))).....))))(((((.....))))) ( -13.50, z-score =  -1.91, R)
>droSim1.chr2R 12525825 51 - 19596830
AGGCGAAAUCGCCUUGUAAGAGGGCGAAACGAGUCUGGAAUUUUUAAUUCC
((((....(((((((.....))))))).....))))(((((.....))))) ( -15.50, z-score =  -2.03, R)
>droSec1.super_1 11278715 51 - 14215200
AGGCGAAAUCGCCUUGUAAGAGGGCGAAACGAGUUUGGAAUUUUUAAUUCC
((((....(((((((.....))))))).....))))(((((.....))))) ( -13.00, z-score =  -1.30, R)
>droYak2.chr2R 5739659 51 + 21139217
AGGCGAAAUCGCCUUGUAAGAGGGCGAAACGAGUUUGGAAUUUUUAAUUCC
((((....(((((((.....))))))).....))))(((((.....))))) ( -13.00, z-score =  -1.30, R)
>droEre2.scaffold_4845 8010806 51 - 22589142
AGGCGAAAUCGCCUUGUAAGAGGGCGAAACGAGUUUGGAAUUUUUAAUUCC
((((....(((((((.....))))))).....))))(((((.....))))) ( -13.00, z-score =  -1.30, R)
>droAna3.scaffold_13266 9477054 51 + 19884421
AAGCGAAAUCGCCUUGUAAGAGGACGAAACGAGUUUGGAAUUUUUAAUUCC
((((....(((((((....)))).))).....))))(((((.....))))) ( -10.40, z-score =  -0.92, R)
>dp4.chr3 6242830 51 - 19779522
AGACGAAAUCGCCUUGUAAGAGGGCGAAACGAGUUUGGAAUUUUUAAUUCC
((((....(((((((.....))))))).....))))(((((.....))))) ( -13.50, z-score =  -1.91, R)
>droPer1.super_2 6457531 51 - 9036312
AGACGAAAUCGCCUUGUAAGAGGGCGAAACGAGUUUGGAAUUUUUAAUUCC
((((....(((((((.....))))))).....))))(((((.....))))) ( -13.50, z-score =  -1.91, R)
>consensus
AGGCGAAAUCGCCUUGUAAGAGGGCGAAACGAGUUUGGAAUUUUUAAUUCC
((((....(((((((.....))))))).....))))(((((.....))))) (-13.04 = -12.71 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:52 2011