Locus 11117

Sequence ID dm3.chr3R
Location 18,765,787 – 18,765,975
Length 188
Max. P 0.855874
window15274 window15275

overview

Window 4

Location 18,765,787 – 18,765,895
Length 108
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 89.00
Shannon entropy 0.17448
G+C content 0.45245
Mean single sequence MFE -35.08
Consensus MFE -26.40
Energy contribution -26.78
Covariance contribution 0.38
Combinations/Pair 1.07
Mean z-score -2.33
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.93
SVM RNA-class probability 0.855874
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18765787 108 + 27905053
CUCACCUUUUGCUCGGUCGUGAGGUGACUA--GCUAAGGUAACUACUGCUUUUCUGAAGCGGUAAUUAAAAGCAAUUUGUAAGUUAAGCCCGAGCAGAGAA-ACACAGACG------
......((((((((((.(...((....)).--(((....(((.(((((((((...))))))))).)))..)))..............).))))))))))..-.........------ ( -31.10, z-score =  -1.59, R)
>droSim1.chr3R 18577061 111 + 27517382
CUCACCUUUUGCUCGGUGGUGAGGUGACUAGAGCUAAGCUAACUACCGCUUUUCUGAAGCGGUAAUUAAAAGCAAUUUGUAAGUUAAGCCCGAGCAGAGAACACACAGAAG------
......((((((((((((((.((....))...)))).(((((((((((((((...)))))))))....(((....)))....))).)))))))))))))............------ ( -35.30, z-score =  -2.51, R)
>droSec1.super_0 19130268 111 + 21120651
CUCACCUUUUGCUCGGUCGUUAGGUGACUAGAGCUAAGCUAACUACCGCUUUUCUGAAGCGGUAAUUAAAAGCAAUUUGUAAGUUAAGUCCGAGCAGAGAACACACAGAAG------
......((((((((((.(.((((....)))).(((....(((.(((((((((...))))))))).)))..)))..............).))))))))))............------ ( -35.10, z-score =  -2.91, R)
>droEre2.scaffold_4820 1167288 114 - 10470090
CUCACCUUUUGCUCGGUCGUGAGGUGACUA--GCUUAGCUAACUACCGCUUUUCUGGAGCGGUAAUUAAAAGCAAUUUGUAAGUUAAGCCGGAGCACAGCAGA-GCAGAGCACACAG
......((((((((.((.(((((....)).--((((((((.((((((((((.....))))))))....(((....))))).)))))))).....))).)).))-))))))....... ( -38.80, z-score =  -2.30, R)
>consensus
CUCACCUUUUGCUCGGUCGUGAGGUGACUA__GCUAAGCUAACUACCGCUUUUCUGAAGCGGUAAUUAAAAGCAAUUUGUAAGUUAAGCCCGAGCAGAGAACACACAGAAG______
......((((((((((...(((..((......(((....(((.((((((((.....)))))))).)))..)))......))..)))...)))))))))).................. (-26.40 = -26.78 +   0.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,765,879 – 18,765,975
Length 96
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 88.80
Shannon entropy 0.17338
G+C content 0.47025
Mean single sequence MFE -25.98
Consensus MFE -21.27
Energy contribution -21.77
Covariance contribution 0.50
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.752864
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18765879 96 - 27905053
GCCGUUAUGAGCGGUCCUUAUAGAAGGACUAAAUAGCCACAGGGCUAUUGGUUAUUAUUCGCCAAAAAUCCGUCCUUCUUC--GUCUGUGUUUCUCUG-----
(((((.....)))))......((((((((..(((((((....)))))))(((........)))........))))))))..--...............----- ( -27.80, z-score =  -2.89, R)
>droSim1.chr3R 18577155 96 - 27517382
GCCGUUAUGAGCGGUCCUUAAAGAAGGACUAAAUAGCCGCAGGACU-CUGGUUAUUAUUCGCCGAAAAUCCGUCCUUCUUCUUCUGUGUGUU-CUCUG-----
(((((.....))))).....(((((((((..((((((((.......-.)))))))).(((...))).....)))))))))............-.....----- ( -22.80, z-score =  -0.96, R)
>droSec1.super_0 19130362 96 - 21120651
GCCGUUAUGAGCGGUCCUUCAAGAAGGACUAAAUAGCCGCAGGACU-CUGGUUAUUAUUCGCCGAAAAUCCGUCCUUCUUCUUCUGUGUGUU-CUCUG-----
(((((.....))))).....(((((((((..((((((((.......-.)))))))).(((...))).....)))))))))............-.....----- ( -22.80, z-score =  -0.85, R)
>droEre2.scaffold_4820 1167380 101 + 10470090
GCCGUUAUGAGCGGUCCUUAAAGAAGGACUAAAUAGCCACAGGGCU-CUGGUUAUUAUUCGCCAAAAAUCCGUCCUUCUUC-UGUGUGCUCUGCUCUGCUGUG
((.((...((((((..(.(((((((((((.....((((....))))-.((((........)))).......))))))))).-))...)..)))))).)).)). ( -30.50, z-score =  -2.60, R)
>consensus
GCCGUUAUGAGCGGUCCUUAAAGAAGGACUAAAUAGCCACAGGACU_CUGGUUAUUAUUCGCCAAAAAUCCGUCCUUCUUC_UCUGUGUGUU_CUCUG_____
(((((.....))))).....(((((((((.....((((....))))..((((........)))).......)))))))))....................... (-21.27 = -21.77 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:36:43 2011