Locus 3839

Sequence ID	3L_DroMel_CAF1
Location	11,092,896 – 11,093,024
Length	128
Max. P	0.963741

overview

Window 6

Location	11,092,896 – 11,092,989
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	96.99
Mean single sequence MFE	-21.58
Consensus MFE	-19.06
Energy contribution	-19.10
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.80
Structure conservation index	0.88
SVM decision value	1.56
SVM RNA-class probability	0.963741
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11092896 93 + 23771897
CGAAACUGAGCUUGCGGCCAGUGUUGCCAACAGGCGAUUACAUGCCACAAAUAGCGAAUAAAUCAUUCAAAGCAGAAAAGAGCUGCAUUAAAA
.........(((((.(((..((((((((....))))).)))..))).))...)))((((.....))))...((((.......))))....... ( -22.60)
>DroSec_CAF1 4002 93 + 1
CCAAACUGAGCUUGCGGCCAGUGUUGCCAACAGGCGAUUACAUGCCACAAAUAGCGAAUAAAUCAUUCAAAGCUGAAAAGAGCUGCAUUAAAA
......((((((((.(((..((((((((....))))).)))..))).)...((((((((.....))))...))))....))))).))...... ( -21.70)
>DroSim_CAF1 4451 93 + 1
CCAAACUGAGCUUGCGGCCAGUGUUGCCAACAGGCGAUUACAUGCCACAAAUAGCGAAUAAAUCAUUCAAAGCUGAAAAGAGCUGCAUUAAAA
......((((((((.(((..((((((((....))))).)))..))).)...((((((((.....))))...))))....))))).))...... ( -21.70)
>DroEre_CAF1 4039 93 + 1
CCAAACUGAGCUUGCGGCCAGUGUUGCCAACAGGCGAUUUCAAGCCACAAAUAGCGAAUAAAUCAUUCAAAGCGGAAAAGAGCUGCAUUAAAA
.........(((((.(((....((((((....)))))).....))).))...)))((((.....))))...((((.......))))....... ( -21.50)
>DroYak_CAF1 4024 93 + 1
CCAAACUGAGCUUGCGGCCAGUGUUGCCAACAGGCGAUUACAUACCACAAAUAGCGGAUAAAUCAUUCAAAGCGGAAAAGAGCUGCAUUAAAA
......(((((((....((.((((((((....))))).)))............((.((........))...))))....))))).))...... ( -20.40)
>consensus
CCAAACUGAGCUUGCGGCCAGUGUUGCCAACAGGCGAUUACAUGCCACAAAUAGCGAAUAAAUCAUUCAAAGCGGAAAAGAGCUGCAUUAAAA
...........(((.(((....((((((....)))))).....))).)))...((((((.....))))..(((........)))))....... (-19.06 = -19.10 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	11,092,911 – 11,093,024
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	95.04
Mean single sequence MFE	-28.76
Consensus MFE	-22.38
Energy contribution	-22.46
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-1.78
Structure conservation index	0.78
SVM decision value	0.16
SVM RNA-class probability	0.613075
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11092911 113 + 23771897
GGCCAGUGUUGCCAACAGGCGAUUACAUGCCACAAAUAGCGAAUAAAUCAUUCAAAGCAGAAAAGAGCUGCAUUAAAAAGUUGUGUCCAUGUGACACUCGAAGGAAAAGCGCC
((((.((((((((....)))))(((((((.(((((.....((((.....))))...((((.......)))).........)))))..))))))))))((....))...).))) ( -30.00)
>DroSec_CAF1 4017 113 + 1
GGCCAGUGUUGCCAACAGGCGAUUACAUGCCACAAAUAGCGAAUAAAUCAUUCAAAGCUGAAAAGAGCUGCAUUAAAAAGUUGUGUCCAUGUGACACUCGAAGGAAAAGCGCC
((((.((((((((....)))))(((((((.(((((.....((((.....))))..((((......))))...........)))))..))))))))))((....))...).))) ( -28.50)
>DroSim_CAF1 4466 113 + 1
GGCCAGUGUUGCCAACAGGCGAUUACAUGCCACAAAUAGCGAAUAAAUCAUUCAAAGCUGAAAAGAGCUGCAUUAAAAAGUUGUGUCCAUGUGACACUCGAAGGAAAAGCGCC
((((.((((((((....)))))(((((((.(((((.....((((.....))))..((((......))))...........)))))..))))))))))((....))...).))) ( -28.50)
>DroEre_CAF1 4054 113 + 1
GGCCAGUGUUGCCAACAGGCGAUUUCAAGCCACAAAUAGCGAAUAAAUCAUUCAAAGCGGAAAAGAGCUGCAUUAAAAAGUUGUGUCCAUGUGACACAUACAGGAAAAGCGCU
(((....((((((....)))))).....)))......((((...............((((.......))))........((((((((.....)))))).))........)))) ( -28.10)
>DroYak_CAF1 4039 113 + 1
GGCCAGUGUUGCCAACAGGCGAUUACAUACCACAAAUAGCGGAUAAAUCAUUCAAAGCGGAAAAGAGCUGCAUUAAAAAGCUGUGGCCAUGUGACACUCAAAGGAAAAGCGCU
((((.((((((((....))))).))).........(((((((((.....))))...((((.......))))........)))))))))..(((....((....))....))). ( -28.70)
>consensus
GGCCAGUGUUGCCAACAGGCGAUUACAUGCCACAAAUAGCGAAUAAAUCAUUCAAAGCGGAAAAGAGCUGCAUUAAAAAGUUGUGUCCAUGUGACACUCGAAGGAAAAGCGCC
(((....((((((....)))))).....))).......((((((.....))))...((.......((((.........))))(((((.....)))))...........)))). (-22.38 = -22.46 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:00 2006