Locus 8773

Sequence ID dm3.chr3R
Location 1,517,173 – 1,517,287
Length 114
Max. P 0.780735
window12044 window12045

overview

Window 4

Location 1,517,173 – 1,517,273
Length 100
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 81.65
Shannon entropy 0.28328
G+C content 0.58463
Mean single sequence MFE -30.07
Consensus MFE -19.75
Energy contribution -20.12
Covariance contribution 0.38
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.780735
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1517173 100 - 27905053
UGAGCCACCGAAGAGCUCGAGGACAGCGGGCUGGCGACGGCGAUGGCGAUGGGGAUGACGAUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGAAGAAAG----
.(((((......).)))).......((((((((....))))..(((((((.(......).)).((((((....)))))).)))))))))...........---- ( -31.80, z-score =  -2.00, R)
>droSim1.chr3R 1551849 94 - 27517382
UGAGCCACGGAAGAGCUCGAGGACAGCGGGCUGGCGAUGGCGAUGGC------GAUGACGAUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGGAGAAAC----
...(((.(....)((((((.......)))))))))....(((.((((------(.........((((((....)))))).))))).)))...........---- ( -30.50, z-score =  -2.39, R)
>droSec1.super_6 1633003 94 - 4358794
UGAGCCACGGAAGAGCUCGAGGACAGCGGGCUGGCGAUGGCGAUGGC------GAUGACGAUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGGAGAAAG----
...(((.(....)((((((.......)))))))))....(((.((((------(.........((((((....)))))).))))).)))...........---- ( -30.50, z-score =  -2.15, R)
>droYak2.chr3R 17483289 83 - 28832112
UAAGCCACGGAAAAGCUCGUGGACAGCGGGGUGGC---------------------GACGUUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGAAGGACCGGAG
...(((((((......)))))).)...(.((((((---------------------(......((((((....)))))).))))))).)............... ( -27.50, z-score =  -1.72, R)
>consensus
UGAGCCACGGAAGAGCUCGAGGACAGCGGGCUGGCGAUGGCGAUGGC______GAUGACGAUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGAAGAAAC____
(((((.........)))))......((((..((((....((....))................((((((....))))))..))))))))............... (-19.75 = -20.12 +   0.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,517,177 – 1,517,287
Length 110
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 86.45
Shannon entropy 0.21448
G+C content 0.60831
Mean single sequence MFE -38.67
Consensus MFE -27.35
Energy contribution -27.85
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.697003
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1517177 110 - 27905053
ACGCAUACGCCGCGUGAGCCACCGAAGAGCUCGAGGACAGCGGGCUGGCGACGGCGAUGGCGAUGGGGAUGACGAUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGAAG
..(((..((((((((.((((........(((.......))).)))).))).))))).(((((((.(......).)).((((((....)))))).))))).)))....... ( -40.10, z-score =  -1.64, R)
>droSim1.chr3R 1551853 104 - 27517382
ACGCAUACGCCGCGUGAGCCACGGAAGAGCUCGAGGACAGCGGGCUGGCGAUGGCGAUGGC------GAUGACGAUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGGAG
..(((..((((((((.((((.(....).(((.......))).)))).))).))))).((((------(.........((((((....)))))).))))).)))....... ( -39.50, z-score =  -2.04, R)
>droSec1.super_6 1633007 104 - 4358794
ACGCAUACGCCGCGUGAGCCACGGAAGAGCUCGAGGACAGCGGGCUGGCGAUGGCGAUGGC------GAUGACGAUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGGAG
..(((..((((((((.((((.(....).(((.......))).)))).))).))))).((((------(.........((((((....)))))).))))).)))....... ( -39.50, z-score =  -2.04, R)
>droYak2.chr3R 17483297 89 - 28832112
ACGCAUACGCCGCGUAAGCCACGGAAAAGCUCGUGGACAGCGGGGUGGC---------------------GACGUUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGAAG
..((.....((((.....((((((......))))))...))))((((((---------------------(......((((((....)))))).)))))))))....... ( -35.60, z-score =  -2.51, R)
>consensus
ACGCAUACGCCGCGUGAGCCACGGAAGAGCUCGAGGACAGCGGGCUGGCGAUGGCGAUGGC______GAUGACGAUGAAGUGCGAAGGCAUUUAUGCCACUGCAGAGAAG
..((((.((((((....))........((((((.......))))))))))...........................((((((....))))))))))............. (-27.35 = -27.85 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:51:54 2011