Locus 9384

Sequence ID dm3.chr3R
Location 6,333,825 – 6,333,930
Length 105
Max. P 0.977600
window12866 window12867

overview

Window 6

Location 6,333,825 – 6,333,930
Length 105
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 91.11
Shannon entropy 0.14802
G+C content 0.39089
Mean single sequence MFE -20.78
Consensus MFE -19.08
Energy contribution -19.12
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.28
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.98
SVM RNA-class probability 0.977600
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6333825 105 + 27905053
CCAUUUUAACAAGUCCUUUGUUAAUUUU----UUUCUGGUGCAUUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCUCCCUAUCCGUCUCUUACCAUUUAUCGCUAGGAUC
.....((((((((...))))))))....----.(((((((((((........))))..((((..(((....))).)))).....................))))))).. ( -20.90, z-score =  -2.41, R)
>droEre2.scaffold_4770 2471063 103 - 17746568
UCAUUUUAACAUGUCCUUUGUUAAUUU-----UUUCUGGUGCACUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCGCCCUAUC-GUCCCUUACCAUUUAUCGCUAGGAUC
.....((((((.......))))))...-----.((((((((((..........)))..(((((.(((....))))))))...-.................))))))).. ( -19.40, z-score =  -1.36, R)
>droYak2.chr3R 10362001 104 + 28832112
UCAUUUUAACAUGUCCUUUGUUAAUUUA----CUUCUGGUGCAUUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCGCCCUAUC-GUCCCUUACCAUUUAUCGCUAGGAUC
.....((((((.......))))))....----.(((((((((((........))))..(((((.(((....))))))))...-.................))))))).. ( -22.00, z-score =  -2.21, R)
>droSec1.super_0 5512915 105 - 21120651
CCAUUUUAACAUUUCCUUUGUUAAUUUUCUUUUUUCUGGUGCAUUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCUCCCUAUC----CCUUACCAUUUAUCGCUAGGAUC
.....((((((.......)))))).........(((((((((((........))))..((((..(((....))).))))...----..............))))))).. ( -20.80, z-score =  -2.97, R)
>droSim1.chr3R 12470778 105 - 27517382
CCAUUUUAACAUUUCCAUUGUUAAUUUUCUUUUUUCUGGUGCAUUUUAGUCUAUGCUCGGGGUUGCAUUUCUGCUCCCUAUC----CCUUACCAUUUAUCGCUAGGAUC
.....((((((.......)))))).........(((((((((((........))))..((((..(((....))).))))...----..............))))))).. ( -20.80, z-score =  -2.45, R)
>consensus
CCAUUUUAACAUGUCCUUUGUUAAUUUU____UUUCUGGUGCAUUUUAGUCUAUGCUCAGGGUUGCAUUUCUGCUCCCUAUC_GUCCCUUACCAUUUAUCGCUAGGAUC
.....((((((.......)))))).........(((((((((((........))))..((((..(((....))).)))).....................))))))).. (-19.08 = -19.12 +   0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,333,825 – 6,333,930
Length 105
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 91.11
Shannon entropy 0.14802
G+C content 0.39089
Mean single sequence MFE -21.20
Consensus MFE -20.18
Energy contribution -20.22
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -2.08
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.94
SVM RNA-class probability 0.975951
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6333825 105 - 27905053
GAUCCUAGCGAUAAAUGGUAAGAGACGGAUAGGGAGCAGAAAUGCAACCCUGAGCAUAGACUAAAAUGCACCAGAAA----AAAAUUAACAAAGGACUUGUUAAAAUGG
...............((((..........(((((.(((....)))..))))).((((........))))))))....----....(((((((.....)))))))..... ( -22.10, z-score =  -2.62, R)
>droEre2.scaffold_4770 2471063 103 + 17746568
GAUCCUAGCGAUAAAUGGUAAGGGAC-GAUAGGGCGCAGAAAUGCAACCCUGAGCAUAGACUAAAGUGCACCAGAAA-----AAAUUAACAAAGGACAUGUUAAAAUGA
..((((.((........)).))))..-..(((((.(((....)))..))))).((((........))))........-----...((((((.......))))))..... ( -21.40, z-score =  -1.77, R)
>droYak2.chr3R 10362001 104 - 28832112
GAUCCUAGCGAUAAAUGGUAAGGGAC-GAUAGGGCGCAGAAAUGCAACCCUGAGCAUAGACUAAAAUGCACCAGAAG----UAAAUUAACAAAGGACAUGUUAAAAUGA
..((((.........((((.......-..(((((.(((....)))..))))).((((........))))))))...(----(......))..))))(((......))). ( -22.50, z-score =  -2.06, R)
>droSec1.super_0 5512915 105 + 21120651
GAUCCUAGCGAUAAAUGGUAAGG----GAUAGGGAGCAGAAAUGCAACCCUGAGCAUAGACUAAAAUGCACCAGAAAAAAGAAAAUUAACAAAGGAAAUGUUAAAAUGG
..((((.((........)).)))----).(((((.(((....)))..))))).((((........))))................((((((.......))))))..... ( -20.90, z-score =  -2.41, R)
>droSim1.chr3R 12470778 105 + 27517382
GAUCCUAGCGAUAAAUGGUAAGG----GAUAGGGAGCAGAAAUGCAACCCCGAGCAUAGACUAAAAUGCACCAGAAAAAAGAAAAUUAACAAUGGAAAUGUUAAAAUGG
..((((.((........)).)))----)...(((.(((....)))...)))..((((........))))................((((((.(....)))))))..... ( -19.10, z-score =  -1.56, R)
>consensus
GAUCCUAGCGAUAAAUGGUAAGGGAC_GAUAGGGAGCAGAAAUGCAACCCUGAGCAUAGACUAAAAUGCACCAGAAA____AAAAUUAACAAAGGACAUGUUAAAAUGG
...............((((..........(((((.(((....)))..))))).((((........))))))))............((((((.......))))))..... (-20.18 = -20.22 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:03:22 2011