Locus 13178

Sequence ID dm3.chrX
Location 4,818,155 – 4,818,277
Length 122
Max. P 0.994825
window18115 window18116

overview

Window 5

Location 4,818,155 – 4,818,277
Length 122
Sequences 3
Columns 123
Reading direction forward
Mean pairwise identity 72.01
Shannon entropy 0.39293
G+C content 0.59943
Mean single sequence MFE -52.80
Consensus MFE -38.91
Energy contribution -39.37
Covariance contribution 0.46
Combinations/Pair 1.20
Mean z-score -2.14
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.15
SVM RNA-class probability 0.983809
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818155 122 + 22422827
GCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCC-GGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCGGGAGCGAACUUGUUGGAGUCAAACUACAGGCUACCAGGGCGCU
..((.((((.((((((((((((..((((..((((((...)))))-)..))))..)))))))))))).))))))((((((..(((....))).((((((((........)))).)))))))))) ( -55.50, z-score =  -4.17, R)
>droSim1.chrX 13316225 122 - 17042790
GCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCC-GCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACGCUGGGGCCCU
((((.(((((.((((((((.((..(.(((.((((((...)))))-).))).)..)).)))))))).))))).))))...((((..((((((....))))))..(..(((....)))..))))) ( -56.80, z-score =  -2.28, R)
>droSec1.super_4 4252194 123 - 6179234
GCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAACUUCAGGCUACCUGGGCGCU
((((..((...(((((..........))))).......(((((((((((.(..((...))..).)))))).))))))).((((((.......((((((.....))))))))).)))))))... ( -46.11, z-score =   0.05, R)
>consensus
GCUCGACCGACGCUGGAGAAUCAAAGCCGGCGGAAGUAACUUCC_GGCGGUUAAGAUACUCCAGCGCCGGUGAAGCGGAAGGAGCGAACUUGUUGGAGUCAAACUACAGGCUACCAGGGCGCU
(((..((((..((((((((.((..(((((.((((((...))))).).)))))..)).))))))))..))))..)))......((((....(.((((((((........)))).)))).))))) (-38.91 = -39.37 +   0.46)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 4,818,155 – 4,818,277
Length 122
Sequences 3
Columns 123
Reading direction reverse
Mean pairwise identity 72.01
Shannon entropy 0.39293
G+C content 0.59943
Mean single sequence MFE -49.81
Consensus MFE -35.12
Energy contribution -34.13
Covariance contribution -0.99
Combinations/Pair 1.22
Mean z-score -2.62
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.74
SVM RNA-class probability 0.994825
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818155 122 - 22422827
AGCGCCCUGGUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCCGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCC-GGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGC
((((((..((.(((.......(((....))).......))))).))))))(((((((((((((((((((..(.(((.(-(((((...)))))).))).)..))))))))))))))))).)).. ( -55.84, z-score =  -5.41, R)
>droSim1.chrX 13316225 122 + 17042790
AGGGCCCCAGCGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGC-GGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGC
(((((......)))))......(((((......))))).........(((..((((..((.((((..((..(((((.(-(((((...)))))).)))))..))..)))).))..))))..))) ( -48.30, z-score =  -1.41, R)
>droSec1.super_4 4252194 123 + 6179234
AGCGCCCAGGUAGCCUGAAGUUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGC
((((...(((.(((..((...(((....)))...))..))))))..))))(((((((.((((((((.((..(.(((.(((((......))))).))).)..)).)))))))).))))).)).. ( -45.30, z-score =  -1.03, R)
>consensus
AGCGCCCAGGUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCUUCCGCUUCACCGGCGCUGGAGAAUCUUAACCGCC_GGAAGUAACUUCCGCCGGCUUAGAUACUCCAGCGUCGGUCGAGC
.((((....))....((.((.....)).))........)).......((((.(((((.((((((((.((....(((.(.(((((...)))))).)))....)).)))))))).))))).)))) (-35.12 = -34.13 +  -0.99)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:08 2011