Locus 5527

Sequence ID dm3.chr3LHet
Location 171,704 – 171,793
Length 89
Max. P 0.904051
window7588

overview

Window 8

Location 171,704 – 171,793
Length 89
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 59.15
Shannon entropy 0.65113
G+C content 0.45034
Mean single sequence MFE -28.88
Consensus MFE -6.25
Energy contribution -10.00
Covariance contribution 3.75
Combinations/Pair 1.39
Mean z-score -2.76
Structure conservation index 0.22
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.904051
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 171704 89 + 2555491
--------GACCUAGCAAAGGGUAAAAAUCUAAAUUACUUUUGUGAUGCUUGCCUUGUGGUUGCGAACGAGAUGAAAUCGUUUAUGCGCCAAACUAA
--------....(((...(((((((..(((((((.....)))).)))..))))))).((((.((((((((.......))))))..))))))..))). ( -20.00, z-score =  -1.35, R)
>dp4.Unknown_group_18 10214 95 - 50799
GCGUAGUCGACCUCAUAAAGACUC--GGUCCCAACUGGACCUGUUGGGACUGCAGAGCGAUUGAGAACGACAUGCUGGUUUUUAUGAGACAGACUCA
..(.((((...((((((((((((.--(((((((((.......)))))))))(((...((........))...))).))))))))))))...))))). ( -37.80, z-score =  -4.19, R)
>droPer1.super_57 65797 95 - 429542
GCGUAGUCGACCUCAUAAAGACUC--GGUCCCAACUGGACCUGUUGGGACUGCAGAGCGAUUGAGAACGACAUGCUGGUUUUUAUGAGACAGACUCA
..(.((((...((((((((((((.--(((((((((.......)))))))))(((...((........))...))).))))))))))))...))))). ( -37.80, z-score =  -4.19, R)
>droWil1.scaffold_181145 88529 83 + 2682060
--------GAUCAAAAAAAG------GGUCUCAAAUUUGGAUGUGAGUCAUGCCGGAUCGUGGAAGAUGAAAUGGAAUUUUUCAUGCGGCAAACAAA
--------((((........------)))).....(((((((....))).(((((...((((((((((........)))))))))))))))..)))) ( -19.90, z-score =  -1.30, R)
>consensus
________GACCUAAUAAAGACUC__GGUCCCAACUGGACCUGUGAGGACUGCAGAGCGAUUGAGAACGACAUGCAAGUUUUUAUGAGACAAACUAA
...........((((((((((((...(((((((((.......)))))))))......((........)).......))))))))))))......... ( -6.25 = -10.00 +   3.75) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:50:08 2011