Locus 5109

Sequence ID dm3.chr2R
Location 17,788,862 – 17,788,952
Length 90
Max. P 0.952505
window7009

overview

Window 9

Location 17,788,862 – 17,788,952
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 93.70
Shannon entropy 0.09926
G+C content 0.56826
Mean single sequence MFE -32.38
Consensus MFE -30.01
Energy contribution -29.20
Covariance contribution -0.81
Combinations/Pair 1.21
Mean z-score -2.08
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.952505
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17788862 90 - 21146708
AGGGGCGUGUCUUUGGGUGUCGCCUACUUUGCAUUUCAAAUGCGCCGUCGCCGUGUCGUUUGUCUCGUCUACAUGGUUGUGGCAAUGCCG
...(((((.....((((.....))))....((((.....))))((((..(((((((((.......))...)))))))..)))).))))). ( -28.90, z-score =  -0.97, R)
>droSim1.chr2R 16424389 90 - 19596830
GGAGGCGUGUCUUUGGGUGUCGCCUACUUUGCAUUUCAAAUGCGCCGUCGCCGUGUCGUUUGUCUCGUCUACAUGGCUGUGGCAAUGCCG
((((((((..(....)..).))))).....((((.....))))((((..(((((((((.......))...)))))))..))))....)). ( -30.70, z-score =  -1.35, R)
>droYak2.chr2R 9743694 90 + 21139217
AGGGGCGUGCCCCUCGGUGUUGCCUACUUUGCAUUUCAAAUGCGCCGUCGCCGUGUCGUUUGUCUCGUCUACAUGGUUGUGGCAAUGCCG
(((((....)))))((((((((((.((...((((.....))))......(((((((((.......))...))))))).)))))))))))) ( -34.70, z-score =  -2.68, R)
>droEre2.scaffold_4845 11922593 89 - 22589142
-GGGGCGUGCCCCUCGGUGUUGCCUACUUUGCAUUUCAAAUGCGCCGUCGCCGUGUCGUUUGUCUCGUCUACAUGGUUGUGGCAAUACCG
-((((....)))).((((((((((.((...((((.....))))......(((((((((.......))...))))))).)))))))))))) ( -35.20, z-score =  -3.31, R)
>consensus
AGGGGCGUGCCCCUCGGUGUCGCCUACUUUGCAUUUCAAAUGCGCCGUCGCCGUGUCGUUUGUCUCGUCUACAUGGUUGUGGCAAUGCCG
.((((....))))..(((((((((.((...((((.....))))......(((((((((.......))...))))))).))))))))))). (-30.01 = -29.20 +  -0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:41:59 2011