Locus 6254

Sequence ID dm3.chr3L
Location 5,014,821 – 5,014,942
Length 121
Max. P 0.753626
window8597 window8598

overview

Window 7

Location 5,014,821 – 5,014,925
Length 104
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 67.01
Shannon entropy 0.50196
G+C content 0.36156
Mean single sequence MFE -16.21
Consensus MFE -9.10
Energy contribution -8.91
Covariance contribution -0.19
Combinations/Pair 1.11
Mean z-score -1.29
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.753626
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5014821 104 + 24543557
UCGAAUAUUUUUCCAAAAUGAUUUCUUUAUUUUAUCAUUAAGGCUUACAGGCACUCUUCCAUUUU-CUUUAGUGCAUCUCAAAGGAUGCCAACUAUCCGGCGGAC
...........(((..((((((...........))))))...(((.....(((((..........-....)))))........(((((.....))))))))))). ( -17.04, z-score =  -0.54, R)
>droSim1.chr3L 4562318 90 + 22553184
-------------UCAAAU-AUUUUAAAAAUAUUUCAUUAAUGUUUUAAGGCACUCUUCCAUUUU-CUUUAGUGCAUCUCAAAGGAUGCCAACUAUCCGGUGGAC
-------------......-......((((((((.....))))))))..........((((((..-...((((((((((....))))))..))))...)))))). ( -16.70, z-score =  -1.94, R)
>droYak2.chr3L 5599507 87 + 24197627
------------------UGAAAUAUUUCUAACUCCCUUACAGUUUAAAAACACUCUUCCAUUUUUCUUGAGUGCAUCUCAAAGGAUGCCAACUAUCAAGCGGAC
------------------...............((((((..((((.......((((.............))))((((((....)))))).))))...))).))). ( -14.02, z-score =  -1.22, R)
>droEre2.scaffold_4784 7728314 87 + 25762168
------------------UCAAAUAUUUUGUACUCCAUUAUAUUUCCAAGACACUAUUCCAUUUUUCUCUAGUGCAUCCGAGAGGAUGCAGACAAUCAGGCGGAC
------------------..((((((..((.....))..))))))............(((............(((((((....)))))))(.....)....))). ( -17.10, z-score =  -1.46, R)
>consensus
__________________UGAAAUAUUUAUUACUCCAUUAAAGUUUAAAGACACUCUUCCAUUUU_CUUUAGUGCAUCUCAAAGGAUGCCAACUAUCAGGCGGAC
.........................................................(((.............((((((....))))))............))). ( -9.10 =  -8.91 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,014,851 – 5,014,942
Length 91
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 80.42
Shannon entropy 0.34350
G+C content 0.45471
Mean single sequence MFE -24.78
Consensus MFE -17.50
Energy contribution -18.50
Covariance contribution 1.00
Combinations/Pair 1.21
Mean z-score -1.46
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.680105
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5014851 91 + 24543557
UUUAUCAUUAAGGCUUACAGGCACUCUUCCAUUUUCUUU-AGUGCAUCUCAAAGGAUGCCAACUAUCCGGCGGACGGGAGUAGAGUGCUGGU
................((.((((((((............-.(.((((((....))))))).(((.((((.....))))))))))))))).)) ( -25.80, z-score =  -1.36, R)
>droSim1.chr3L 4562337 88 + 22553184
---UUCAUUAAUGUUUUAAGGCACUCUUCCAUUUUCUUU-AGUGCAUCUCAAAGGAUGCCAACUAUCCGGUGGACGGGAGUAGGGUGCUGGU
---................((((((((............-.(.((((((....))))))).(((.((((.....)))))))))))))))... ( -24.60, z-score =  -1.25, R)
>droSec1.super_2 4994830 88 + 7591821
---UUCAAUAAAGUUUUAAGGCACUCUUCCAUUUUCUUU-AGUGCAUCUCAAAGGAUGCCAACUAUCCGGCGGACGGGAGUAGAGUGCUGGU
---................((((((((............-.(.((((((....))))))).(((.((((.....)))))))))))))))... ( -25.50, z-score =  -1.81, R)
>droYak2.chr3L 5599522 89 + 24197627
---UCCCUUACAGUUUAAAAACACUCUUCCAUUUUUCUUGAGUGCAUCUCAAAGGAUGCCAACUAUCAAGCGGACGGGAGUAGAGUGCUGGC
---.......(((........(((((((((..((..(((((..((((((....))))))......)))))..))..)))..))))))))).. ( -22.90, z-score =  -1.02, R)
>droEre2.scaffold_4784 7728329 84 + 25762168
---UCCAUUAUAUUUCCAAGACACUAUUCCAUUUUUCUCUAGUGCAUCCGAGAGGAUGCAGACAAUCAGGCGGACGGGUGU-----GCUGGC
---............(((..(((((..(((............(((((((....)))))))(.....)....)))..)))))-----..))). ( -25.10, z-score =  -1.85, R)
>consensus
___UUCAUUAAAGUUUAAAGGCACUCUUCCAUUUUCUUU_AGUGCAUCUCAAAGGAUGCCAACUAUCCGGCGGACGGGAGUAGAGUGCUGGU
...................(((((((((((.((..((...(((((((((....))))))..)))....))..)).)))...))))))))... (-17.50 = -18.50 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:04:07 2011