Locus 3235

Sequence ID	dm3.chr2R
Location	3,632,473 – 3,632,572
Length	99
Max. P	0.985291

overview

Window 9

Location	3,632,473 – 3,632,572
Length	99
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	94.44
Shannon entropy	0.08767
G+C content	0.63131
Mean single sequence MFE	-40.00
Consensus MFE	-36.55
Energy contribution	-37.05
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	0.91
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.20
SVM RNA-class probability	0.985291
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3632473 99 + 21146708
GGAGGAAGUGAAGGAAGCCGAGGAAGCGGUGGGUGGCGGAUUGGGGUGGCUGGUGCCCACAAUUGGCGCCUACUGAACGCGACUAAGCGACUCCGACGG
((((......................(((((((((.(.(((((((((.......)))).))))).))))))))))..(((......))).))))..... ( -37.60, z-score =  -1.36, R)
>droEre2.scaffold_4929 7665540 99 - 26641161
GGAGGAAGUGGAGGAAGCGGAGGAGGCGGUGGGUGGCGGAUUGGGGUGGGUGGUGCCCACAAUUGGCGCCUACUGAAGGCGACUAAGCGACUCCGACUG
......(((((((...((..((..(.(((((((((.(.(((((((((.......)))).))))).))))))))))....)..))..))..)))).))). ( -41.20, z-score =  -3.28, R)
>droSec1.super_1 1287662 99 + 14215200
GACGGAAUUGAAGGAAGCGGAGGAAGCGGUGGGUGGCGGAUUGGGGUGGGUGGUGCCCACAAUUGGCGCCUACUGAACGCGACUAAGCGACUCCGACUG
...............(((((((....(((((((((.(.(((((((((.......)))).))))).))))))))))..(((......))).))))).)). ( -40.50, z-score =  -3.12, R)
>droSim1.chr2R 2363282 99 + 19596830
GACGGAAUUGAAGGAAGCGGAGGAAGCGGUGGGUGGCGGAUUGGGGUGGGUGGUGCCCACAAUUGGCGCCUACUGAACGCGACUGAGCGACUCCGACUG
..((((.(((..((..(((.......(((((((((.(.(((((((((.......)))).))))).))))))))))..)))..))...))).)))).... ( -40.70, z-score =  -3.09, R)
>consensus
GAAGGAAGUGAAGGAAGCGGAGGAAGCGGUGGGUGGCGGAUUGGGGUGGGUGGUGCCCACAAUUGGCGCCUACUGAACGCGACUAAGCGACUCCGACUG
.................(((((....(((((((((.(.(((((((((.......)))).))))).))))))))))..(((......))).))))).... (-36.55 = -37.05 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	3,632,473 – 3,632,572
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	94.44
Shannon entropy	0.08767
G+C content	0.63131
Mean single sequence MFE	-24.56
Consensus MFE	-21.08
Energy contribution	-21.39
Covariance contribution	0.31
Combinations/Pair	1.05
Mean z-score	-1.69
Structure conservation index	0.86
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.20
SVM RNA-class probability	0.591510
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3632473 99 - 21146708
CCGUCGGAGUCGCUUAGUCGCGUUCAGUAGGCGCCAAUUGUGGGCACCAGCCACCCCAAUCCGCCACCCACCGCUUCCUCGGCUUCCUUCACUUCCUCC
(((..((((((((......))).......((((...((((.(((.........))))))).)))).......)))))..)))................. ( -23.90, z-score =  -0.37, R)
>droEre2.scaffold_4929 7665540 99 + 26641161
CAGUCGGAGUCGCUUAGUCGCCUUCAGUAGGCGCCAAUUGUGGGCACCACCCACCCCAAUCCGCCACCCACCGCCUCCUCCGCUUCCUCCACUUCCUCC
.((.(((((..((...(.(((((.....))))).)....(((((.....)))))..................))...)))))))............... ( -24.90, z-score =  -2.51, R)
>droSec1.super_1 1287662 99 - 14215200
CAGUCGGAGUCGCUUAGUCGCGUUCAGUAGGCGCCAAUUGUGGGCACCACCCACCCCAAUCCGCCACCCACCGCUUCCUCCGCUUCCUUCAAUUCCGUC
.((.(((((.(((......))).......((((......(((((.....))))).......))))............)))))))............... ( -24.72, z-score =  -1.93, R)
>droSim1.chr2R 2363282 99 - 19596830
CAGUCGGAGUCGCUCAGUCGCGUUCAGUAGGCGCCAAUUGUGGGCACCACCCACCCCAAUCCGCCACCCACCGCUUCCUCCGCUUCCUUCAAUUCCGUC
.((.(((((.(((......))).......((((......(((((.....))))).......))))............)))))))............... ( -24.72, z-score =  -1.96, R)
>consensus
CAGUCGGAGUCGCUUAGUCGCGUUCAGUAGGCGCCAAUUGUGGGCACCACCCACCCCAAUCCGCCACCCACCGCUUCCUCCGCUUCCUUCAAUUCCGCC
.....((((..((..((..(((....((.((((......(((((.....))))).......))))))....)))...))..))...))))......... (-21.08 = -21.39 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:06:22 2011