Locus 9913

Sequence ID dm3.chr3R
Location 9,766,701 – 9,766,828
Length 127
Max. P 0.635687
window13621 window13622

overview

Window 1

Location 9,766,701 – 9,766,796
Length 95
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 87.08
Shannon entropy 0.22227
G+C content 0.55612
Mean single sequence MFE -34.48
Consensus MFE -29.56
Energy contribution -30.82
Covariance contribution 1.26
Combinations/Pair 1.12
Mean z-score -1.30
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.635687
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9766701 95 + 27905053
UGAUGAUGGGACUGGUGAUGAUGGGUCUCUGGC----------GGGGAUCUGGGCCGAGACUGGCCAAUUGUUUCGGCCAGUUUGAGCAGCUAAAA-----AAGAACGCG
.......((((((.((....)).))))))..((----------(....(((.(((((((((.........)))))))))((((.....))))....-----.))).))). ( -29.80, z-score =  -0.78, R)
>droEre2.scaffold_4770 5882966 103 - 17746568
UGAUGAUGAGACUGGUGAUGAUGGGUC--UGGCGAGGAUUGCCGUGGAUCUGGGCCGGGACUGGCCAAUUGUUUCGGCCUGGUCGAGCAGCAAAAA-----AAGAACGCG
........(((((.((....)).))))--).(((....((((.((.((((.((((((..((.........))..))))))))))..)).))))...-----.....))). ( -34.00, z-score =  -1.07, R)
>droYak2.chr3R 14082012 108 + 28832112
CGAUGAUGGGACUGGUGAUGAUGGGUC--UGGCGAGGAUUGCCGGGGAUCUGGGCUGAGACUGGCCAAUUGUUUCGGCCAGAUCGAGCUGCAAAAACAAAAAAGAACGCG
........(((((.((....)).))))--).(((.((....))...(((((((.(((((((.........))))))))))))))......................))). ( -32.00, z-score =  -0.74, R)
>droSec1.super_0 8877367 105 - 21120651
UGAUGAUGGGACUGGUGAUGAUGGGUCUCUGGCAAGGAUUGCCGGGGAUCUGGGCCAAGACUGGCCAAUUGUUUCGGCCAGGUUGUGCAGCUGAAA-----AAGAACGCG
...........(((((((..((((((((((((((.....)))))))))))).(((((....))))).))..))...)))))...(((...((....-----.))..))). ( -37.80, z-score =  -1.80, R)
>droSim1.chr3R 15856811 105 - 27517382
UGAUGAUGGGACUGGUGAUGAUGGGUCUCUGGCGAGGAUUGCCGGGGAUCUGGGCCGAGACUGGCCAAUUGUUUCGGCCAGGUUGUGCAGCUGAAA-----AAGAACGCG
......(.((.((((..((...(((((((((((((...))))))))))))).(((((((((.........)))))))))..))..).))))).)..-----......... ( -38.80, z-score =  -2.10, R)
>consensus
UGAUGAUGGGACUGGUGAUGAUGGGUCUCUGGCGAGGAUUGCCGGGGAUCUGGGCCGAGACUGGCCAAUUGUUUCGGCCAGGUUGAGCAGCUAAAA_____AAGAACGCG
..............(((.....(((((((((((((...))))))))))))).(((((((((.........)))))))))...........................))). (-29.56 = -30.82 +   1.26)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,766,733 – 9,766,828
Length 95
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 90.90
Shannon entropy 0.15615
G+C content 0.51430
Mean single sequence MFE -26.86
Consensus MFE -22.23
Energy contribution -22.55
Covariance contribution 0.32
Combinations/Pair 1.13
Mean z-score -1.52
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr3R 9766733 95 - 27905053
CCACUUAUUGUCCCCGGGAUUUUUAUCUUUAUCGCGUUCUU-----UUUUAGCUGCUCAAACUGGCCGAAACAAUUGGCCAGUCUCGGCCCAGAUCCCCG---
...............(((((((...........((......-----.....)).(((.(.(((((((((.....))))))))).).)))..)))))))..--- ( -25.60, z-score =  -2.56, R)
>droEre2.scaffold_4770 5883003 98 + 17746568
CCACUGAUUGUCCCCGGGAUUUUUAUCUUUAUCGCGUUCUU-----UUUUUGCUGCUCGACCAGGCCGAAACAAUUGGCCAGUCCCGGCCCAGAUCCACGGCA
((...((((....((((((((..........(((.((....-----........)).)))...((((((.....))))))))))))))....))))...)).. ( -27.60, z-score =  -1.21, R)
>droYak2.chr3R 14082049 103 - 28832112
CCACUGAUUGUCCCCGGGAUUUUUAUCUUUAUCGCGUUCUUUUUUGUUUUUGCAGCUCGAUCUGGCCGAAACAAUUGGCCAGUCUCAGCCCAGAUCCCCGGCA
............((.(((((((...........(((..(......)....))).(((.((.((((((((.....))))))))..)))))..))))))).)).. ( -28.30, z-score =  -1.79, R)
>droSec1.super_0 8877406 98 + 21120651
CCACUGAUUGUCCCCGGGAUUUUUAUCUUUAUCGCGUUCUU-----UUUCAGCUGCACAACCUGGCCGAAACAAUUGGCCAGUCUUGGCCCAGAUCCCCGGCA
............((.(((((((...........((......-----.....)).((.(((.((((((((.....))))))))..)))))..))))))).)).. ( -27.00, z-score =  -1.22, R)
>droSim1.chr3R 15856850 98 + 27517382
CCACUGAUUGUCCCCGGGAUUUUUAUCUUUAUCGCGUUCUU-----UUUCAGCUGCACAACCUGGCCGAAACAAUUGGCCAGUCUCGGCCCAGAUCCCCGGCA
............((.(((((((...........((......-----.....)).((.....((((((((.....)))))))).....))..))))))).)).. ( -25.80, z-score =  -0.84, R)
>consensus
CCACUGAUUGUCCCCGGGAUUUUUAUCUUUAUCGCGUUCUU_____UUUUAGCUGCUCAACCUGGCCGAAACAAUUGGCCAGUCUCGGCCCAGAUCCCCGGCA
.............(((((((((...........((................)).(((.(..((((((((.....))))))))..).)))..)))))).))).. (-22.23 = -22.55 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:13:48 2011