Locus 11489

Sequence ID dm3.chr3R
Location 21,558,685 – 21,558,750
Length 65
Max. P 0.580739
window15790 window15791

overview

Window 0

Location 21,558,685 – 21,558,750
Length 65
Sequences 5
Columns 65
Reading direction forward
Mean pairwise identity 63.85
Shannon entropy 0.67353
G+C content 0.37544
Mean single sequence MFE -13.37
Consensus MFE -6.72
Energy contribution -5.92
Covariance contribution -0.80
Combinations/Pair 1.68
Mean z-score -0.54
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.580739
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21558685 65 + 27905053
UUAAAAAGAUCCCAUUCUUUGGAAUCACCAAAGAAGGUGGGAAUCUGUAUUUUAGGCAGGGUUGG
.........(((((((((((((.....)))))))..)))))).(((((.......)))))..... ( -20.00, z-score =  -2.44, R)
>droSim1.chr2h_random 793290 65 + 3178526
GAGAAAAAGUCCAACUCUUUUUCUUCUUCAGUAAAGGUGGGAACUUGUAUUUUUGGUAAUACUUU
(((((((((.......))))))))).........((((....))))(((((......)))))... ( -10.00, z-score =   0.40, R)
>droSec1.super_80 44630 65 + 135508
AAGAAUAAGUCCCACUAUUUGACUUCUCCAGUAAAGGUAGGAACUUGUAUUUUUGGUUAUACAGG
.........(((.(((.....(((.....)))...))).))).(((((((........))))))) (  -9.70, z-score =   0.78, R)
>droEre2.scaffold_4784 616793 65 - 25762168
GAGAAUAAUUCCCAUUCUUUUCCUUCUCCAGUAAAGGUGGGAACUUGUAUUUUUGGUAAUACAGG
........(((((((.((((.(........).)))))))))))((((((((......)))))))) ( -15.80, z-score =  -1.40, R)
>triCas2.singleUn_1817 15298 58 - 22356
CUGAAUGCUAACCAUUUUUCGUAUGCACCGUCGAAAGUGGGCAAGUCAAUUUUGGGUA-------
...........(((.........(((.(((.(....))))))).........)))...------- ( -11.37, z-score =  -0.05, R)
>consensus
GAGAAUAAGUCCCAUUCUUUGUCUUCUCCAGUAAAGGUGGGAACUUGUAUUUUUGGUAAUACAGG
(((((((((((((((.((((............))))))))).))))..))))))........... ( -6.72 =  -5.92 +  -0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 21,558,685 – 21,558,750
Length 65
Sequences 5
Columns 65
Reading direction reverse
Mean pairwise identity 63.85
Shannon entropy 0.67353
G+C content 0.37544
Mean single sequence MFE -11.90
Consensus MFE -4.76
Energy contribution -4.20
Covariance contribution -0.56
Combinations/Pair 1.64
Mean z-score -0.99
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.518681
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21558685 65 - 27905053
CCAACCCUGCCUAAAAUACAGAUUCCCACCUUCUUUGGUGAUUCCAAAGAAUGGGAUCUUUUUAA
...........(((((...((((.((((..((((((((.....))))))))))))))))))))). ( -17.80, z-score =  -3.38, R)
>droSim1.chr2h_random 793290 65 - 3178526
AAAGUAUUACCAAAAAUACAAGUUCCCACCUUUACUGAAGAAGAAAAAGAGUUGGACUUUUUCUC
...(((((......)))))((((.((.((((((.((.....))..)))).)).))))))...... (  -8.70, z-score =  -0.08, R)
>droSec1.super_80 44630 65 - 135508
CCUGUAUAACCAAAAAUACAAGUUCCUACCUUUACUGGAGAAGUCAAAUAGUGGGACUUAUUCUU
...((((........))))((((.(((((..(((((.....)))..))..)))))))))...... ( -10.50, z-score =  -0.07, R)
>droEre2.scaffold_4784 616793 65 + 25762168
CCUGUAUUACCAAAAAUACAAGUUCCCACCUUUACUGGAGAAGGAAAAGAAUGGGAAUUAUUCUC
..((((((......))))))(((((((((((((......))))).......))))))))...... ( -15.21, z-score =  -1.68, R)
>triCas2.singleUn_1817 15298 58 + 22356
-------UACCCAAAAUUGACUUGCCCACUUUCGACGGUGCAUACGAAAAAUGGUUAGCAUUCAG
-------..........(((..((((((.(((((..........)))))..)))...))).))). (  -7.30, z-score =   0.26, R)
>consensus
CCAGUAUUACCAAAAAUACAAGUUCCCACCUUUACUGGAGAAGACAAAGAAUGGGAAUUAUUCUC
...................(((((((...((((............))))...)))))))...... ( -4.76 =  -4.20 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:43:56 2011