Locus 9450

Sequence ID	dm3.chr3R
Location	6,762,542 – 6,762,621
Length	79
Max. P	0.976076

overview

Window 9

Location	6,762,542 – 6,762,621
Length	79
Sequences	4
Columns	80
Reading direction	forward
Mean pairwise identity	74.63
Shannon entropy	0.41602
G+C content	0.59456
Mean single sequence MFE	-18.98
Consensus MFE	-9.54
Energy contribution	-10.85
Covariance contribution	1.31
Combinations/Pair	1.19
Mean z-score	-1.73
Structure conservation index	0.50
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.09
SVM RNA-class probability	0.537153
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 6762542 79 + 27905053
CAGUAUCCACUGUCCAUUGCCCACUGUUCACUGCCCAGUUUUCACUGUCCAAUGUCCGC-CGUCCGGUGCUCAGUGCCCA
.......(((((..(((((..(..((..((.((..((((....))))..)).))..)).-.)..)))))..))))).... ( -17.80, z-score =  -1.77, R)
>droSec1.super_0 5930549 79 - 21120651
CAGUAGCCACUGUCCAUUGCCCACUGUCCACUGCCCAGUUUCCACUGUCCAAUGUCCGU-CGUCCGGUGCUCAGUGCCCA
.......(((((..(((((..(..((..((.((..((((....))))..)).))..)).-.)..)))))..))))).... ( -18.10, z-score =  -1.41, R)
>droEre2.scaffold_4770 2901427 72 - 17746568
-------CAGUGUCCACUAUCCACCACCCAGUGUUCAGUGCCCAGUGUCCAGUGUCCGC-UGUCCGGUGCUCAGUGCCCA
-------...((..((((...((((...(((((..((.((.........)).))..)))-))...))))...))))..)) ( -18.80, z-score =  -1.53, R)
>dp4.chr2 7173564 78 + 30794189
CCGUCUCCGCUGUCCAGUGUCCGCUGUCCAAGGUCCAGUGUCCACUGUACACUGUCCGCCUGUCCAGU--UCAAUGGCCA
........(((((.(((((..(((((.(....)..)))))..))))).))((((..(....)..))))--.....))).. ( -21.20, z-score =  -2.21, R)
>consensus
CAGUAUCCACUGUCCAUUGCCCACUGUCCACUGCCCAGUGUCCACUGUCCAAUGUCCGC_CGUCCGGUGCUCAGUGCCCA
.......(((((..(((((..(..((..((.((..((((....))))..)).))..))...)..)))))..))))).... ( -9.54 = -10.85 +   1.31)

alignment

secondary structure

dotplot

Window 0

Location	6,762,542 – 6,762,621
Length	79
Sequences	4
Columns	80
Reading direction	reverse
Mean pairwise identity	74.63
Shannon entropy	0.41602
G+C content	0.59456
Mean single sequence MFE	-25.73
Consensus MFE	-16.12
Energy contribution	-16.12
Covariance contribution	0.00
Combinations/Pair	1.29
Mean z-score	-2.21
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.94
SVM RNA-class probability	0.976076
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 6762542 79 - 27905053
UGGGCACUGAGCACCGGACG-GCGGACAUUGGACAGUGAAAACUGGGCAGUGAACAGUGGGCAAUGGACAGUGGAUACUG
((..(((((....(((....-.))).(((((..((((....))))..)))))..)))))..)).....((((....)))) ( -24.10, z-score =  -1.96, R)
>droSec1.super_0 5930549 79 + 21120651
UGGGCACUGAGCACCGGACG-ACGGACAUUGGACAGUGGAAACUGGGCAGUGGACAGUGGGCAAUGGACAGUGGCUACUG
(((.(((((....(((..(.-(((..(((((..((((....))))..)))))..).)).)....))).))))).)))... ( -28.80, z-score =  -3.04, R)
>droEre2.scaffold_4770 2901427 72 + 17746568
UGGGCACUGAGCACCGGACA-GCGGACACUGGACACUGGGCACUGAACACUGGGUGGUGGAUAGUGGACACUG-------
.((((.....)).))...((-(.(..(((((..(((....((((.(....).)))))))..)))))..).)))------- ( -22.40, z-score =  -1.04, R)
>dp4.chr2 7173564 78 - 30794189
UGGCCAUUGA--ACUGGACAGGCGGACAGUGUACAGUGGACACUGGACCUUGGACAGCGGACACUGGACAGCGGAGACGG
((.(((.((.--.(((..((((.(..((((((.......))))))..)))))..)))....)).))).)).((....)). ( -27.60, z-score =  -2.81, R)
>consensus
UGGGCACUGAGCACCGGACA_GCGGACAUUGGACAGUGGAAACUGGACAGUGGACAGUGGACAAUGGACAGUGGAUACUG
....(((((....(((......))).(((((..((((....))))..)))))..)))))..................... (-16.12 = -16.12 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:04:39 2011