Locus 4548

Sequence ID dm3.chr2R
Location 13,915,816 – 13,915,940
Length 124
Max. P 0.991852
window6232 window6233 window6234 window6235

overview

Window 2

Location 13,915,816 – 13,915,924
Length 108
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 91.52
Shannon entropy 0.11687
G+C content 0.62795
Mean single sequence MFE -44.27
Consensus MFE -36.60
Energy contribution -36.27
Covariance contribution -0.33
Combinations/Pair 1.08
Mean z-score -1.90
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.702957
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13915816 108 + 21146708
GCGCCAAGGAGCUGGCAGGCAGGAUGGGUU--UGGGAUGCGCUGAGGAGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCAGGAGCAAACGAGUUAAGUGC
((((.....((((.((((((.......)))--))...(((.((..((.(((((((.((((((..(((...))))))))).))))))))).)).)))..).))))..)))) ( -42.20, z-score =  -1.74, R)
>droSim1.chr2R 12654507 110 + 19596830
GCGCCAAGGAGCAGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGCUGGGGUCCUUGGGCUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGC
.((((((....(..(....)..).....))))))...(..(((((((((((((((.((((((..(((...))))))))).))))))))))))).))..)........... ( -47.50, z-score =  -2.14, R)
>droSec1.super_1 11409439 110 + 14215200
GCGCCAAGGAGCAGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGAUGGGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGC
.((((((....(..(....)..).....))))))...(..(((..((((((((((.((((((..(((...))))))))).))))))))))...)))..)........... ( -43.10, z-score =  -1.82, R)
>consensus
GCGCCAAGGAGCAGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGAUGGGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGC
(((((........))).........................((...(((((((((.((((((..(((...))))))))).))))))))).)).))............... (-36.60 = -36.27 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,915,816 – 13,915,924
Length 108
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 91.52
Shannon entropy 0.11687
G+C content 0.62795
Mean single sequence MFE -36.03
Consensus MFE -32.69
Energy contribution -32.80
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.52
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.09
SVM RNA-class probability 0.981868
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13915816 108 - 21146708
GCACUUAACUCGUUUGCUCCUGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCUCCUCAGCGCAUCCCA--AACCCAUCCUGCCUGCCAGCUCCUUGGCGC
((.............(((...(((((((((.(((((((((...)))..)))))).)))))))))...)))........--..............(((((....))))))) ( -36.20, z-score =  -2.56, R)
>droSim1.chr2R 12654507 110 - 19596830
GCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGCCCAAGGACCCCAGCACAUCCCCCCACCAACCCAUCCUGCCUGCCUGCUCCUUGGCGC
((.........(..((.(((.(((((((((.(.(((((((...)))..)))).).))))))))).)))))..).....................(((........))))) ( -35.70, z-score =  -2.02, R)
>droSec1.super_1 11409439 110 - 14215200
GCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCCCAUCACAUCCCCCCACCAACCCAUCCUGCCUGCCUGCUCCUUGGCGC
((.........(..((.((..(((((((((.(((((((((...)))..)))))).)))))))))..))))..).....................(((........))))) ( -36.20, z-score =  -2.97, R)
>consensus
GCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCCCAUCACAUCCCCCCACCAACCCAUCCUGCCUGCCUGCUCCUUGGCGC
((...................(((((((((.(((((((((...)))..)))))).)))))))))..............................(((........))))) (-32.69 = -32.80 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,915,828 – 13,915,940
Length 112
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 90.35
Shannon entropy 0.13473
G+C content 0.56756
Mean single sequence MFE -43.07
Consensus MFE -34.86
Energy contribution -34.53
Covariance contribution -0.33
Combinations/Pair 1.07
Mean z-score -2.03
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763965
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13915828 112 + 21146708
UGGCAGGCAGGAUGGGUU--UGGGAUGCGCUGAGGAGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCAGGAGCAAACGAGUUAAGUGCGCUCUAAAAUAUGUAG
......(((.......((--(((..((((((..((.(((((((.((((((..(((...))))))))).)))))))))...(((......))).))))))..)))))...))).. ( -42.20, z-score =  -2.38, R)
>droSim1.chr2R 12654519 114 + 19596830
AGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGCUGGGGUCCUUGGGCUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGCGCUCUAAAAUAUGUAA
...(((.(......).))).((((((..(((((((((((((((.((((((..(((...))))))))).))))))))))))).))..)..((.....)).))))).......... ( -45.70, z-score =  -2.13, R)
>droSec1.super_1 11409451 114 + 14215200
AGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGAUGGGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGCGCUCUAAUAUAUGUAC
...(((.(......).))).((((((..(((..((((((((((.((((((..(((...))))))))).))))))))))...)))..)..((.....)).))))).......... ( -41.30, z-score =  -1.57, R)
>consensus
AGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGAUGGGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGCGCUCUAAAAUAUGUAA
..(((........((((............((...(((((((((.((((((..(((...))))))))).))))))))).)).(((...........))))))).......))).. (-34.86 = -34.53 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,915,828 – 13,915,940
Length 112
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 90.35
Shannon entropy 0.13473
G+C content 0.56756
Mean single sequence MFE -33.98
Consensus MFE -31.05
Energy contribution -31.17
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.81
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.50
SVM RNA-class probability 0.991852
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13915828 112 - 21146708
CUACAUAUUUUAGAGCGCACUUAACUCGUUUGCUCCUGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCUCCUCAGCGCAUCCCA--AACCCAUCCUGCCUGCCA
............(((((.((.......)).)))))..(((((((((.(((((((((...)))..)))))).)))))))))..(((.(((.....--.........))))))... ( -35.44, z-score =  -3.25, R)
>droSim1.chr2R 12654519 114 - 19596830
UUACAUAUUUUAGAGCGCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGCCCAAGGACCCCAGCACAUCCCCCCACCAACCCAUCCUGCCUGCCU
..........(((.(((((...........)))(((.(((((((((.(.(((((((...)))..)))).).))))))))).)))......................)))))... ( -32.30, z-score =  -2.15, R)
>droSec1.super_1 11409451 114 - 14215200
GUACAUAUAUUAGAGCGCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCCCAUCACAUCCCCCCACCAACCCAUCCUGCCUGCCU
..........(((.(((((...((....))...))).(((((((((.(((((((((...)))..)))))).)))))))))..........................)))))... ( -34.20, z-score =  -3.03, R)
>consensus
CUACAUAUUUUAGAGCGCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCCCAUCACAUCCCCCCACCAACCCAUCCUGCCUGCCU
..........(((.(((((...........)))....(((((((((.(((((((((...)))..)))))).)))))))))..........................)))))... (-31.05 = -31.17 +   0.11)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:31:17 2011