Locus 3538

Sequence ID dm3.chr2R
Location 6,139,289 – 6,139,352
Length 63
Max. P 0.880159
window4854

overview

Window 4

Location 6,139,289 – 6,139,352
Length 63
Sequences 6
Columns 63
Reading direction reverse
Mean pairwise identity 65.11
Shannon entropy 0.68946
G+C content 0.47898
Mean single sequence MFE -16.03
Consensus MFE -6.01
Energy contribution -6.48
Covariance contribution 0.48
Combinations/Pair 1.50
Mean z-score -1.58
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.880159
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6139289 63 - 21146708
CAUAUGGGCCACAGCGAACCGGAAGUAAAGUCUUCGGACUUCACUUUCGGACAUUGGAAUACC
((.(((.((....))...((((((((.(((((....))))).)))))))).)))))....... ( -21.80, z-score =  -3.77, R)
>droSim1.chr2R 4763435 63 - 19596830
CAUUUGGGCCACAGCGAACCGGAAGUAAAGUCUUCGGCCUUCACUUUCGGACAUUGGAAUUCC
..((..(((....))...((((((((.(((.(....).))).))))))))...)..))..... ( -16.70, z-score =  -0.95, R)
>droSec1.super_1 3745848 63 - 14215200
CAUUAGGGCCACAGCGAACCGGAAGUAAAGUCUUCGGGCUUCACUUUCGGACAUUGGAAUUCC
.....((((....))...((((((((.(((((....))))).))))))))...........)) ( -20.60, z-score =  -2.71, R)
>droYak2.chr2L 18765129 61 - 22324452
CAAAUGGGGCAUAUUAGUCCGGAAGU--ACUCUUCAGGCCUUACUUUCCGACCUCGGAAUACC
....((((((.....(((.(....).--)))......))))))..(((((....))))).... ( -16.50, z-score =  -1.34, R)
>droEre2.scaffold_4929 18401638 61 + 26641161
CAUAUGGGCCAAGCCAAACCGGAAGU--AUGCUUCAUGCUUUACUUUCGCACUUUGGAAUACC
.....((......(((((.(((((((--(.((.....))..))))))))...)))))....)) ( -15.30, z-score =  -1.62, R)
>droAna3.scaffold_13266 4603192 53 - 19884421
----------CUGAUUGCCCGGAAAUCGAAUUGGAAAGAAAGUUUCCUGAACUAUGGAAUACC
----------........(((....(((....(((((.....))))))))....)))...... (  -5.30, z-score =   0.88, R)
>consensus
CAUAUGGGCCACAGCGAACCGGAAGUAAAGUCUUCAGGCUUCACUUUCGGACAUUGGAAUACC
..................((((((((....((....))....))))))))............. ( -6.01 =  -6.48 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:12:03 2011