Locus 13180

Sequence ID dm3.chrX
Location 4,818,675 – 4,818,834
Length 159
Max. P 0.999518
window18119 window18120 window18121 window18122

overview

Window 9

Location 4,818,675 – 4,818,794
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.33
Shannon entropy 0.37424
G+C content 0.59211
Mean single sequence MFE -46.03
Consensus MFE -35.24
Energy contribution -35.80
Covariance contribution 0.56
Combinations/Pair 1.17
Mean z-score -2.37
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.46
SVM RNA-class probability 0.991174
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818675 119 + 22422827
GGCCCCCCAGUAUCCUGUAGUUGGACUCAAACAAGUCCCUCC-UUCCGCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAA
(((....(((....))).....(((((......)))))....-....)))..((((.((((((((((((..((((..((((((...))))))..))))..)))))))))))).))))... ( -44.60, z-score =  -3.66, R)
>droSim1.chrX 13315912 120 - 17042790
GGCGCCCUGGUAGCCUGUAGUUUGACUCCAACAAGCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGA
((((....((.(((....((((((.......)))))).)))))...))))(((((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)) ( -47.30, z-score =  -2.01, R)
>droSec1.super_4 4252681 119 - 6179234
-GGGCCCCAGUGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAA
-((((......)))).((((..(((((......))))).......))))((.((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..)))))). ( -46.20, z-score =  -1.44, R)
>consensus
GGCGCCCCAGUAUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCCGCUCGACCGACGCUGGAGAAUCAAAGCCGGCGGAAGUAACUUCCGGCGGUUAAGAUACUCCAGCGCCGGUGAA
......................(((((......)))))..............((((..((((((((.((..(((((.((((((...)))))).)))))..)).))))))))..))))... (-35.24 = -35.80 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,818,675 – 4,818,794
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.33
Shannon entropy 0.37424
G+C content 0.59211
Mean single sequence MFE -51.23
Consensus MFE -38.12
Energy contribution -38.80
Covariance contribution 0.68
Combinations/Pair 1.17
Mean z-score -2.41
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.42
SVM RNA-class probability 0.990394
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818675 119 - 22422827
UUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGCGGAA-GGAGGGACUUGUUUGAGUCCAACUACAGGAUACUGGGGGGCC
.(((((((((((((((((((..(.(((.((((((...)))))).))).)..))))))))))))))))).))((....-....((((((....))))))..(..(((....)))..).)). ( -55.10, z-score =  -4.54, R)
>droSim1.chrX 13315912 120 + 17042790
UCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGCUUGUUGGAGUCAAACUACAGGCUACCAGGGCGCC
............((((..((..(((((.((((((...)))))).)))))..))..)))).((((((((...((.......)).(((((((.(........).))))))))))..))))). ( -48.00, z-score =  -1.19, R)
>droSec1.super_4 4252681 119 + 6179234
UUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACACUGGGGCCC-
((((((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).))).....(((..((((((....))))))..(..(((....)))..))))- ( -50.60, z-score =  -1.50, R)
>consensus
UUCACCGGCGCUGGAGAAUCUUAACCGCCGGAAGUAACUUCCGCCGGCUUAGAUACUCCAGCGUCGGUCGAGCGGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGAUACUGGGGCGCC
...(((((.((((((((.((....(((.((((((...)))))).)))....)).)))))))).)))))..............((((((....))))))..((.(((....))).)).... (-38.12 = -38.80 +   0.68)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,818,714 – 4,818,834
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.78
Shannon entropy 0.38189
G+C content 0.58333
Mean single sequence MFE -55.30
Consensus MFE -48.31
Energy contribution -49.77
Covariance contribution 1.45
Combinations/Pair 1.15
Mean z-score -3.78
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.76
SVM RNA-class probability 0.999283
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818714 120 + 22422827
UCCUUCCGCUCGACAGACGCUGGAAAAUCAAAGCCAGCGGAAGUGACUUCCGGCGGUUAAGAUUUUCCAGCGCCUGUGAAGCGCCGGGAGCGAACUUGUUGGAGUCAAACUACAGGCUAC
((((..((((..((((.((((((((((((..((((..((((((...))))))..))))..)))))))))))).))))..))))..)))).....(((((.(........).))))).... ( -52.30, z-score =  -4.09, R)
>droSim1.chrX 13315952 120 - 17042790
UCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGGAGGGACUUGUUGGAGUCCAACUACAGGACGC
((((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).))))))..((((((....))))))............. ( -57.50, z-score =  -3.50, R)
>droSec1.super_4 4252720 120 - 6179234
CCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGAGCGAGAUUGUUGGAGUCAAACUUCAGGCUAC
.(((((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..)))))))))(((.......((((((.....))))))))).. ( -56.11, z-score =  -3.75, R)
>consensus
UCCUUCCGCUCGACCGACGCUGGAGAAUCAAAGCCGGCGGAAGUAACUUCCGGCGGUUAAGAUACUCCAGCGCCGGUGAAGCGGAAGGAGCGAACUUGUUGGAGUCAAACUACAGGCUAC
.(((((((((..((((..((((((((.((..(((((.((((((...)))))).)))))..)).))))))))..))))..)))))))))......(((((.(........).))))).... (-48.31 = -49.77 +   1.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,818,714 – 4,818,834
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.78
Shannon entropy 0.38189
G+C content 0.58333
Mean single sequence MFE -54.73
Consensus MFE -45.51
Energy contribution -46.63
Covariance contribution 1.12
Combinations/Pair 1.18
Mean z-score -4.16
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.97
SVM RNA-class probability 0.999518
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4818714 120 - 22422827
GUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCCGGCGCUUCACAGGCGCUGGAAAAUCUUAACCGCCGGAAGUCACUUCCGCUGGCUUUGAUUUUCCAGCGUCUGUCGAGCGGAAGGA
...(((.(.(((..((((......)))).))).).)))((((.(((((((((((((((((..(.(((.((((((...)))))).))).)..))))))))))))))))).))))....... ( -55.40, z-score =  -5.02, R)
>droSim1.chrX 13315952 120 + 17042790
GCGUCCUGUAGUUGGACUCCAACAAGUCCCUCCCUUCUGCUCGACCGAAGCCGGAGCAUCGAAGCCGGCGGAAGUAGCUUCCGGCGGUUAAGAAACUCCAGCGCCGGUGAAGCGGAAGGA
.............(((((......)))))...(((((((((..((((..((.((((..((..(((((.((((((...)))))).)))))..))..)))).))..))))..))))))))). ( -56.80, z-score =  -3.75, R)
>droSec1.super_4 4252720 120 + 6179234
GUAGCCUGAAGUUUGACUCCAACAAUCUCGCUCCUUCCGCUUCACCGGCGCUGGAGUUUCUUAACCGCCGGAAGCUACUUCCGCCGGCUUCGAUGCUCCGGCUUCGGUCGAGCAGAAGGG
..(((..((...(((....)))...))..)))(((((.((((.(((((.((((((((.((..(.(((.((((((...)))))).))).)..)).)))))))).))))).)))).))))). ( -52.00, z-score =  -3.70, R)
>consensus
GUAGCCUGUAGUUUGACUCCAACAAGUUCGCUCCUUCCGCUUCACCGGCGCUGGAGAAUCUUAACCGCCGGAAGUAACUUCCGCCGGCUUAGAUACUCCAGCGUCGGUCGAGCGGAAGGA
................................((((((((((.(((((.((((((((.((....(((.((((((...)))))).)))....)).)))))))).))))).)))))))))). (-45.51 = -46.63 +   1.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:13 2011