Locus 11928

Sequence ID dm3.chr3R
Location 24,551,995 – 24,552,095
Length 100
Max. P 0.871627
window16393 window16394

overview

Window 3

Location 24,551,995 – 24,552,095
Length 100
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 87.62
Shannon entropy 0.22723
G+C content 0.49924
Mean single sequence MFE -24.96
Consensus MFE -16.72
Energy contribution -17.80
Covariance contribution 1.08
Combinations/Pair 1.10
Mean z-score -2.46
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.871627
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24551995 100 + 27905053
AUACGAAAUACCGAAUCCGCAAUCCAGAAUCCAGCAGAAUCCGGCUGCUGUCCAUAAUUUGCCUC-----GCAAUUAACAGCCCCUCAUCCAGCUGGUCCGUCGG
..........((((....((((.........((((((.......))))))........))))...-----........((((..........)))).....)))) ( -19.53, z-score =  -0.41, R)
>droEre2.scaffold_4820 6998905 105 - 10470090
AUACGAAAUGCCAAAUCCGGAAUCCGUAAUCCAGAAUCCGGAUUCUGCUGUCCAUAAUUUGCCUCUCUGCGCAAUUAACAGCCCCUCAUCCAGCCGGUCCGUCGG
...(((...(((.((((((((.((.(.....).)).))))))))..(((((...((((((((......))).)))))))))).............)))...))). ( -27.20, z-score =  -2.52, R)
>droYak2.chr3R 6894730 105 - 28832112
AUACGAAACACCGAAUCCGGAAUCCAGAAUCCAAAAUCCGGAUUCUGCUGUCCAUAAUUUGCCUCUCUGCGCAAUUAACAACCCCUCAUCCAGCUGGUACAUCGG
..........((((..(((((...((((((((.......))))))))...))).....(((((.....).)))).....................))....)))) ( -24.60, z-score =  -2.85, R)
>droSec1.super_4 3433556 105 + 6179234
AUACGAAAUACCGAAUCCGGAAUCCAGAAUCCAAAAUCCGGAUUCUGCUGUCCAUAAUUUGCCUCUCUGCGCAAUUAACAGCCCCUCAUCCAGCUGGUCCGUCAG
....((...((((((((((((...............))))))))).(((((...((((((((......))).)))))))))).............)))...)).. ( -26.06, z-score =  -3.11, R)
>droSim1.chr3R 24250747 98 + 27517382
AUACGAAAUACCGAAUCCGGAAUCCAGAAUCC-------GGAUUCUGCUGUCCAUAAUUUGCCUCUCUGCGCAAUUAACAGCCCCUCAUCCAGCUGGUCCGUCAG
....((...((((((((((((........)))-------)))))).(((((...((((((((......))).)))))))))).............)))...)).. ( -27.40, z-score =  -3.42, R)
>consensus
AUACGAAAUACCGAAUCCGGAAUCCAGAAUCCAAAAUCCGGAUUCUGCUGUCCAUAAUUUGCCUCUCUGCGCAAUUAACAGCCCCUCAUCCAGCUGGUCCGUCGG
....((...(((......(((...((((((((.......))))))))...))).....((((........)))).....................)))...)).. (-16.72 = -17.80 +   1.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,551,995 – 24,552,095
Length 100
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 87.62
Shannon entropy 0.22723
G+C content 0.49924
Mean single sequence MFE -34.18
Consensus MFE -26.27
Energy contribution -27.68
Covariance contribution 1.41
Combinations/Pair 1.12
Mean z-score -2.01
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.847800
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24551995 100 - 27905053
CCGACGGACCAGCUGGAUGAGGGGCUGUUAAUUGC-----GAGGCAAAUUAUGGACAGCAGCCGGAUUCUGCUGGAUUCUGGAUUGCGGAUUCGGUAUUUCGUAU
....(((((((((.((((..((.((((((..((((-----...))))......))))))..))..)))).)))))..))))...((((((........)))))). ( -32.60, z-score =  -1.25, R)
>droEre2.scaffold_4820 6998905 105 + 10470090
CCGACGGACCGGCUGGAUGAGGGGCUGUUAAUUGCGCAGAGAGGCAAAUUAUGGACAGCAGAAUCCGGAUUCUGGAUUACGGAUUCCGGAUUUGGCAUUUCGUAU
...(((((...(((.........((((((..((((........))))......)))))).(((((((((.((((.....)))).))))))))))))..))))).. ( -37.10, z-score =  -2.64, R)
>droYak2.chr3R 6894730 105 + 28832112
CCGAUGUACCAGCUGGAUGAGGGGUUGUUAAUUGCGCAGAGAGGCAAAUUAUGGACAGCAGAAUCCGGAUUUUGGAUUCUGGAUUCCGGAUUCGGUGUUUCGUAU
.(((..((((.((((.((((....(((((..((.....))..))))).))))...)))).(((((((((.((..(...)..)).)))))))))))))..)))... ( -35.60, z-score =  -2.46, R)
>droSec1.super_4 3433556 105 - 6179234
CUGACGGACCAGCUGGAUGAGGGGCUGUUAAUUGCGCAGAGAGGCAAAUUAUGGACAGCAGAAUCCGGAUUUUGGAUUCUGGAUUCCGGAUUCGGUAUUUCGUAU
...(((((((..(.....)..))((((((..((((........))))......)))))).(((((((((.((..(...)..)).))))))))).....))))).. ( -34.00, z-score =  -2.02, R)
>droSim1.chr3R 24250747 98 - 27517382
CUGACGGACCAGCUGGAUGAGGGGCUGUUAAUUGCGCAGAGAGGCAAAUUAUGGACAGCAGAAUCC-------GGAUUCUGGAUUCCGGAUUCGGUAUUUCGUAU
...(((((((..(.....)..))((((((..((((........))))......)))))).((((((-------(((........))))))))).....))))).. ( -31.60, z-score =  -1.68, R)
>consensus
CCGACGGACCAGCUGGAUGAGGGGCUGUUAAUUGCGCAGAGAGGCAAAUUAUGGACAGCAGAAUCCGGAUUCUGGAUUCUGGAUUCCGGAUUCGGUAUUUCGUAU
...(((((...(((((((..(((((((((..((((........))))......))))))((((((((.....))))))))....)))..)))))))..))))).. (-26.27 = -27.68 +   1.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:52:22 2011