Locus 1743

Sequence ID dm3.chr2L
Location 13,467,775 – 13,467,916
Length 141
Max. P 0.820989
window2392 window2393 window2394

overview

Window 2

Location 13,467,775 – 13,467,879
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 98.72
Shannon entropy 0.01766
G+C content 0.57692
Mean single sequence MFE -40.40
Consensus MFE -36.70
Energy contribution -40.03
Covariance contribution 3.33
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.556692
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13467775 104 + 23011544
GCAUAACGCGUUGCUCUUUCGAUUUCCACCUGGCCGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGACCUGCCAGAGGCAGAGCCACCUGUCAU
(((........)))................((((.((.(((((...((((((((..(....)..)))).)))).....(((((...)))))))))))).)))). ( -37.70, z-score =  -1.11, R)
>droSim1.chr2L 13250044 104 + 22036055
GCAUAAGGCGUUGCUCUUUCGAUUUCCACCUGGCCGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAU
......(((((.(((((.(((.....)..(((((.(((((((.....(((((((..(....)..)))).)))))))))).))))).)).))))).))..))).. ( -42.10, z-score =  -1.67, R)
>droSec1.super_16 1613781 104 + 1878335
GCAUAACGCGUUGCUCUUUCGAUUUCCACCUGGCCGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAU
.....(((.((.(((((.(((.....)..(((((.(((((((.....(((((((..(....)..)))).)))))))))).))))).)).))))).)).)))... ( -41.40, z-score =  -1.86, R)
>consensus
GCAUAACGCGUUGCUCUUUCGAUUUCCACCUGGCCGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAU
(((........)))...............(((((.(((((((.....(((((((..(....)..)))).)))))))))).))))).(((((......))))).. (-36.70 = -40.03 +   3.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,467,809 – 13,467,916
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 95.02
Shannon entropy 0.06866
G+C content 0.56075
Mean single sequence MFE -40.50
Consensus MFE -33.86
Energy contribution -36.53
Covariance contribution 2.67
Combinations/Pair 1.09
Mean z-score -2.22
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.820989
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13467809 107 + 23011544
CGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGACCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAUGGUAAUGGGAAGGAGAAGGGAAUCGG
.......(((((((((((((..(....)..)))).))((((...(((((...))))))))).(((.(((((..(((...)))..)))))..)))......))))))) ( -39.80, z-score =  -2.24, R)
>droSim1.chr2L 13250078 107 + 22036055
CGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAUGGGAAUGGGAAUGGUAGGGGAAUUGG
....((((((((((((((((..(....)..)))).))))..)))(((((...))))))))))(((..((((.((((.........)))).))))..)))........ ( -42.40, z-score =  -2.76, R)
>droSec1.super_16 1613815 107 + 1878335
CGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAUGGGAAUGGGAAUGGGAAGGCAAUUGG
.(((((((.....(((((((..(....)..)))).))))))))))((((...(((...))).(((((((((.((((...)))).))))...)))))..))))..... ( -39.30, z-score =  -1.66, R)
>consensus
CGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAUGGGAAUGGGAAUGGGAAGGGAAUUGG
(((.(((((...((((((((..(....)..)))).)))).....(((((...))))))))))(((.(((((.((((.........)))).)))))..)))...))). (-33.86 = -36.53 +   2.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,467,809 – 13,467,916
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 95.02
Shannon entropy 0.06866
G+C content 0.56075
Mean single sequence MFE -25.33
Consensus MFE -25.20
Energy contribution -25.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.02
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.704486
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13467809 107 - 23011544
CCGAUUCCCUUCUCCUUCCCAUUACCAUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGUCAGCCAGUCAACCAGUCACCCAGUCGCUGAAUCAGCCAUCCG
..(((((..................(((...))).....(((.(((((((......(((((......)))))......)))))))..)))...)))))......... ( -25.60, z-score =  -1.05, R)
>droSim1.chr2L 13250078 107 - 22036055
CCAAUUCCCCUACCAUUCCCAUUCCCAUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUCAGCCAUCCG
.......................................(((.(((((((......(((((......)))))......)))))))..)))((((...))))...... ( -25.20, z-score =  -1.30, R)
>droSec1.super_16 1613815 107 - 1878335
CCAAUUGCCUUCCCAUUCCCAUUCCCAUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUCAGCCAUCCG
.......................................(((.(((((((......(((((......)))))......)))))))..)))((((...))))...... ( -25.20, z-score =  -0.70, R)
>consensus
CCAAUUCCCUUCCCAUUCCCAUUCCCAUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUCAGCCAUCCG
.......................................(((.(((((((......(((((......)))))......)))))))..)))((((...))))...... (-25.20 = -25.20 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:37:56 2011