Locus 11106

Sequence ID dm3.chr3R
Location 18,717,470 – 18,717,544
Length 74
Max. P 0.998307
window15254 window15255

overview

Window 4

Location 18,717,470 – 18,717,544
Length 74
Sequences 6
Columns 81
Reading direction forward
Mean pairwise identity 71.56
Shannon entropy 0.51858
G+C content 0.50720
Mean single sequence MFE -23.08
Consensus MFE -16.61
Energy contribution -19.78
Covariance contribution 3.17
Combinations/Pair 1.19
Mean z-score -2.41
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.32
SVM RNA-class probability 0.998307
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18717470 74 + 27905053
-------AAAAAAAAAAACAACCAUUCCACCCACUUCUCCGUCGGCGGGAAUGACUGUCGAUAUUGGCAUCCAGUGGGCUG
-------......................((((((...((((((((((......))))))))...)).....))))))... ( -20.20, z-score =  -1.75, R)
>droSim1.chr3R 18528733 71 + 27517382
----------AAAAAAAACACCCAAUCCACCCACUUCUCCGUCGGCGGGAAUGACUGUCGAUAUUGGAGUUCAGUGGGUGG
----------................(((((((((.((((((((((((......))))))))...))))...))))))))) ( -32.80, z-score =  -5.08, R)
>droSec1.super_0 19082719 71 + 21120651
----------AAAAAAAACACCCAUUCCACCCACUUCUCCGUCGGCGGGAAUGACUGUCGAUAUUGGAGUUCAGUGGGUGG
----------................(((((((((.((((((((((((......))))))))...))))...))))))))) ( -32.80, z-score =  -4.95, R)
>droYak2.chr3R 19571630 69 + 28832112
------------AAAAAACACCCAUUCCACCCACUUCUCCGUCGGCCGGAAUGACUGUCGAUAUUGGAGUCCAGCAGAUGG
------------.........(((((......(((((...((((((.(......).))))))...)))))......))))) ( -15.90, z-score =  -0.50, R)
>droEre2.scaffold_4820 1119591 68 - 10470090
-------------AAAAACACCCACUCCACCCACUUCUCCGUCGGCAGGAAUGACUGUCGAUAUUGGAGUCCAGUGAAUGG
-------------.............(((..((((.((((((((((((......))))))))...))))...))))..))) ( -23.10, z-score =  -2.91, R)
>droVir3.scaffold_12822 3928804 81 - 4096053
AUACAAUGACUGUCGAUUAAGCCAGUGCACCCACAUUACCGCUUACGUGAGAGACACUUGACUACUGGCCGCCGUGAGUUG
...(((((.((.(((..(((((.((((......))))...)))))..))).)).)).)))...(((.((....)).))).. ( -13.70, z-score =   0.75, R)
>consensus
__________AAAAAAAACACCCAUUCCACCCACUUCUCCGUCGGCGGGAAUGACUGUCGAUAUUGGAGUCCAGUGGGUGG
..........................(((((((((.((((((((((((......))))))))...))))...))))))))) (-16.61 = -19.78 +   3.17) 

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 5

Location 18,717,470 – 18,717,544
Length 74
Sequences 6
Columns 81
Reading direction reverse
Mean pairwise identity 71.56
Shannon entropy 0.51858
G+C content 0.50720
Mean single sequence MFE -22.07
Consensus MFE -14.53
Energy contribution -14.48
Covariance contribution -0.05
Combinations/Pair 1.50
Mean z-score -1.00
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.85
SVM RNA-class probability 0.835258
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18717470 74 - 27905053
CAGCCCACUGGAUGCCAAUAUCGACAGUCAUUCCCGCCGACGGAGAAGUGGGUGGAAUGGUUGUUUUUUUUUUU-------
(((....)))((((....))))((((..((((((.(((.((......)).)))))))))..)))).........------- ( -22.50, z-score =  -1.43, R)
>droSim1.chr3R 18528733 71 - 27517382
CCACCCACUGAACUCCAAUAUCGACAGUCAUUCCCGCCGACGGAGAAGUGGGUGGAUUGGGUGUUUUUUUU----------
(((((((((...((((....(((.(.(......).).))).)))).)))))))))................---------- ( -22.80, z-score =  -1.40, R)
>droSec1.super_0 19082719 71 - 21120651
CCACCCACUGAACUCCAAUAUCGACAGUCAUUCCCGCCGACGGAGAAGUGGGUGGAAUGGGUGUUUUUUUU----------
(((((((((...((((....(((.(.(......).).))).)))).)))))))))................---------- ( -22.80, z-score =  -1.37, R)
>droYak2.chr3R 19571630 69 - 28832112
CCAUCUGCUGGACUCCAAUAUCGACAGUCAUUCCGGCCGACGGAGAAGUGGGUGGAAUGGGUGUUUUUU------------
(((.....)))...........((((.((((((((.((.((......)).)))))))))).))))....------------ ( -21.80, z-score =  -0.75, R)
>droEre2.scaffold_4820 1119591 68 + 10470090
CCAUUCACUGGACUCCAAUAUCGACAGUCAUUCCUGCCGACGGAGAAGUGGGUGGAGUGGGUGUUUUU-------------
(((((((((...((((....(((.(((......))).))).)))).))))))))).............------------- ( -22.00, z-score =  -0.98, R)
>droVir3.scaffold_12822 3928804 81 + 4096053
CAACUCACGGCGGCCAGUAGUCAAGUGUCUCUCACGUAAGCGGUAAUGUGGGUGCACUGGCUUAAUCGACAGUCAUUGUAU
..(((((((...(((.((......(((.....)))....)))))..)))))))(((.(((((........))))).))).. ( -20.50, z-score =  -0.09, R)
>consensus
CCACCCACUGGACUCCAAUAUCGACAGUCAUUCCCGCCGACGGAGAAGUGGGUGGAAUGGGUGUUUUUUUU__________
(((((((((...((((..........(((.........))))))).))))))))).......................... (-14.53 = -14.48 +  -0.05) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:36:27 2011