Locus 6386

Sequence ID	dm3.chr3L
Location	6,232,865 – 6,232,926
Length	61
Max. P	0.985684

overview

Window 7

Location	6,232,865 – 6,232,926
Length	61
Sequences	6
Columns	61
Reading direction	forward
Mean pairwise identity	84.70
Shannon entropy	0.30019
G+C content	0.50959
Mean single sequence MFE	-17.37
Consensus MFE	-13.47
Energy contribution	-15.00
Covariance contribution	1.53
Combinations/Pair	1.05
Mean z-score	-1.57
Structure conservation index	0.78
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.71
SVM RNA-class probability	0.795708
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6232865 61 + 24543557
GGUUCUUGGCUCUGGGUAAUUAACUCCGUCUCUGACGGAGAUUGUCGUGCUACGCCAGAUG
.....(((((....((((..((((((((((...))))))).)))...))))..)))))... ( -20.30, z-score =  -2.23, R)
>droAna3.scaffold_13337 2584871 51 - 23293914
GGUUCUUUUCUCCGGCUAAUUAACUCCCUUCCUGAUACAGAU-GCACUGAUG---------
((.........))........................(((..-...)))...--------- (  -1.40, z-score =   2.18, R)
>droEre2.scaffold_4784 8920799 61 + 25762168
GGUUCUUGGCUCUGGGUAAUUAACUCCGUCUCUGACGGAGAUUGUGGUGCUAUGCCAGAUG
.....(((((....((((..((((((((((...))))))).)))...))))..)))))... ( -21.00, z-score =  -2.63, R)
>droYak2.chr3L 6812999 61 + 24197627
GGUUCUUGGCUGUGGGUAAUUAACUCCGUCUCUGACGGAGAUUGUGGUGCUACGCCAGAUG
.....(((((.((((.((..((((((((((...))))))).)))...)))))))))))... ( -20.90, z-score =  -2.28, R)
>droSec1.super_2 6198831 61 + 7591821
GGUUCUUGGCUCUGGGUAAUUAACUCCGUCUCUGACGGAGAUUGUCGUGCUACGCCAGAUG
.....(((((....((((..((((((((((...))))))).)))...))))..)))))... ( -20.30, z-score =  -2.23, R)
>droSim1.chr3L 5726428 61 + 22553184
GGUUCUUGGCUCUGGGUAAUUAACUCCGUCUCUGACGGAGAUUGUCGUGCUACGCCAGAUG
.....(((((....((((..((((((((((...))))))).)))...))))..)))))... ( -20.30, z-score =  -2.23, R)
>consensus
GGUUCUUGGCUCUGGGUAAUUAACUCCGUCUCUGACGGAGAUUGUCGUGCUACGCCAGAUG
.....(((((....((((..((((((((((...))))))).)))...))))..)))))... (-13.47 = -15.00 +   1.53)

alignment

secondary structure

dotplot

Window 8

Location	6,232,865 – 6,232,926
Length	61
Sequences	6
Columns	61
Reading direction	reverse
Mean pairwise identity	84.70
Shannon entropy	0.30019
G+C content	0.50959
Mean single sequence MFE	-15.23
Consensus MFE	-11.21
Energy contribution	-12.24
Covariance contribution	1.03
Combinations/Pair	1.09
Mean z-score	-2.61
Structure conservation index	0.74
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.21
SVM RNA-class probability	0.985684
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6232865 61 - 24543557
CAUCUGGCGUAGCACGACAAUCUCCGUCAGAGACGGAGUUAAUUACCCAGAGCCAAGAACC
..(((((.((((.........(((((((...)))))))....))))))))).......... ( -17.92, z-score =  -3.26, R)
>droAna3.scaffold_13337 2584871 51 + 23293914
---------CAUCAGUGC-AUCUGUAUCAGGAAGGGAGUUAAUUAGCCGGAGAAAAGAACC
---------.........-.(((...((.((....((.....))..)).))....)))... (  -3.80, z-score =   1.62, R)
>droEre2.scaffold_4784 8920799 61 - 25762168
CAUCUGGCAUAGCACCACAAUCUCCGUCAGAGACGGAGUUAAUUACCCAGAGCCAAGAACC
..((((((.............(((((((...))))))).............))).)))... ( -16.37, z-score =  -3.64, R)
>droYak2.chr3L 6812999 61 - 24197627
CAUCUGGCGUAGCACCACAAUCUCCGUCAGAGACGGAGUUAAUUACCCACAGCCAAGAACC
..((((((.............(((((((...))))))).............))).)))... ( -17.47, z-score =  -3.84, R)
>droSec1.super_2 6198831 61 - 7591821
CAUCUGGCGUAGCACGACAAUCUCCGUCAGAGACGGAGUUAAUUACCCAGAGCCAAGAACC
..(((((.((((.........(((((((...)))))))....))))))))).......... ( -17.92, z-score =  -3.26, R)
>droSim1.chr3L 5726428 61 - 22553184
CAUCUGGCGUAGCACGACAAUCUCCGUCAGAGACGGAGUUAAUUACCCAGAGCCAAGAACC
..(((((.((((.........(((((((...)))))))....))))))))).......... ( -17.92, z-score =  -3.26, R)
>consensus
CAUCUGGCGUAGCACGACAAUCUCCGUCAGAGACGGAGUUAAUUACCCAGAGCCAAGAACC
....((((.............(((((((...))))))).............))))...... (-11.21 = -12.24 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:06:45 2011