Locus 7309

Sequence ID dm3.chr3L
Location 13,773,092 – 13,773,207
Length 115
Max. P 0.972428
window10059 window10060

overview

Window 9

Location 13,773,092 – 13,773,207
Length 115
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 80.35
Shannon entropy 0.38061
G+C content 0.50498
Mean single sequence MFE -37.60
Consensus MFE -22.56
Energy contribution -26.45
Covariance contribution 3.89
Combinations/Pair 1.07
Mean z-score -2.45
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972428
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13773092 115 + 24543557
CUCACUUUCCCGCUUACACUCUCUGCUGGUUAUUGGCAGAGAGUGGCAG-AGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUC
...........(((..((((((((((..(...)..))))))))))...(-((((((((.(.((((...(((((.....))))).)))).).))).)))))).........)))... ( -41.10, z-score =  -3.53, R)
>droEre2.scaffold_4784 13779548 115 + 25762168
CUGACUUUCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAG-AGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUC
...........(((..((((((((((..(...)..))))))))))...(-((((((((.(.((((...(((((.....))))).)))).).))).)))))).........)))... ( -41.10, z-score =  -2.94, R)
>droYak2.chr3L 13871249 115 + 24197627
CUCACUUUCCCGCUUACACUCUCGACUGGCCAUUGGCAGAGAGUGGCAG-AGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUC
...........(((..(((((((.....(((...))).)))))))...(-((((((((.(.((((...(((((.....))))).)))).).))).)))))).........)))... ( -35.40, z-score =  -1.55, R)
>droSec1.super_0 5934664 115 + 21120651
CUCACUUGCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAG-AGUGUGGCCGUUGUCCUUGUUUUUCCUGUAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUC
......((((.((...((((((((((..(...)..)))))))))))).(-((((((((.(.((((...((((.......)))).)))).).))).)))))).........)))).. ( -42.70, z-score =  -3.58, R)
>droSim1.chr3L 13159797 115 + 22553184
CUCACUUGCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAG-AGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUC
......((((.((...((((((((((..(...)..)))))))))))).(-((((((((.(.((((...(((((.....))))).)))).).))).)))))).........)))).. ( -44.10, z-score =  -3.55, R)
>droGri2.scaffold_15110 17759884 89 + 24565398
------------------------AAAGGCUUUGGCCAGGCGCCAGAAACACCGACGCCAUCGUCCUCGCAUUGGUUUGG---UUACAGGCCCCAACACUUAAUUAAAAUGGCAUC
------------------------...(((....)))....((((........((((....))))........((((((.---...)))))).................))))... ( -21.20, z-score =   0.48, R)
>consensus
CUCACUUUCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAG_AGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUC
..........((((..(((((((((((.......))))))))))).....))))..((((((......(((((.....)))))((((....))))............))))))... (-22.56 = -26.45 +   3.89)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,773,092 – 13,773,207
Length 115
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 80.35
Shannon entropy 0.38061
G+C content 0.50498
Mean single sequence MFE -36.03
Consensus MFE -21.08
Energy contribution -23.34
Covariance contribution 2.25
Combinations/Pair 1.19
Mean z-score -1.57
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.555433
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13773092 115 - 24543557
GAUGCCAUUUUAAUUAAGUGUUGGCGGAUGCCAGUUUCCAGGAAAAACAAGGACAACGGCCACACU-CUGCCACUCUCUGCCAAUAACCAGCAGAGAGUGUAAGCGGGAAAGUGAG
.....((((((.....(((((.(((.(.((((.((((.......))))..)).)).).))))))))-((((((((((((((.........))))))))))...)))).)))))).. ( -38.60, z-score =  -2.80, R)
>droEre2.scaffold_4784 13779548 115 - 25762168
GAUGCCAUUUUAAUUAAGUGUUGGCGGAUGCCAGUUUCCAGGAAAAACAAGGACAACGGCCACACU-CUGCCACUCUCUGCCAAUGGCCAGCAGAGAGUGUAAGCGGGAAAGUCAG
(((.((..........(((((.(((.(.((((.((((.......))))..)).)).).))))))))-.(((((((((((((.........))))))))))...)))))...))).. ( -36.90, z-score =  -1.55, R)
>droYak2.chr3L 13871249 115 - 24197627
GAUGCCAUUUUAAUUAAGUGUUGGCGGAUGCCAGUUUCCAGGAAAAACAAGGACAACGGCCACACU-CUGCCACUCUCUGCCAAUGGCCAGUCGAGAGUGUAAGCGGGAAAGUGAG
.....((((((.....(((((.(((.(.((((.((((.......))))..)).)).).))))))))-(((((((((((.(((...))).....)))))))...)))).)))))).. ( -33.40, z-score =  -0.52, R)
>droSec1.super_0 5934664 115 - 21120651
GAUGCCAUUUUAAUUAAGUGUUGGCGGAUGCCAGUUUACAGGAAAAACAAGGACAACGGCCACACU-CUGCCACUCUCUGCCAAUGGCCAGCAGAGAGUGUAAGCGGGCAAGUGAG
..((((..........(((((.(((.(.((((.((((.......))))..)).)).).))))))))-.(((((((((((((.........))))))))))...)))))))...... ( -39.00, z-score =  -1.96, R)
>droSim1.chr3L 13159797 115 - 22553184
GAUGCCAUUUUAAUUAAGUGUUGGCGGAUGCCAGUUUCCAGGAAAAACAAGGACAACGGCCACACU-CUGCCACUCUCUGCCAAUGGCCAGCAGAGAGUGUAAGCGGGCAAGUGAG
..((((..........(((((.(((.(.((((.((((.......))))..)).)).).))))))))-.(((((((((((((.........))))))))))...)))))))...... ( -38.70, z-score =  -1.64, R)
>droGri2.scaffold_15110 17759884 89 - 24565398
GAUGCCAUUUUAAUUAAGUGUUGGGGCCUGUAA---CCAAACCAAUGCGAGGACGAUGGCGUCGGUGUUUCUGGCGCCUGGCCAAAGCCUUU------------------------
(((((((((........(((((((.........---.....)))))))......)))))))))(((((.....))))).(((....)))...------------------------ ( -29.58, z-score =  -0.94, R)
>consensus
GAUGCCAUUUUAAUUAAGUGUUGGCGGAUGCCAGUUUCCAGGAAAAACAAGGACAACGGCCACACU_CUGCCACUCUCUGCCAAUGGCCAGCAGAGAGUGUAAGCGGGAAAGUGAG
................(((((.(((.(.((((..................)).)).).)))))))).((((((((((((((.........))))))))))...))))......... (-21.08 = -23.34 +   2.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:24:26 2011