Locus 6398

Sequence ID	3L_DroMel_CAF1
Location	17,139,157 – 17,139,247
Length	90
Max. P	0.942374

overview

Window 1

Location	17,139,157 – 17,139,247
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	93.78
Mean single sequence MFE	-30.65
Consensus MFE	-26.34
Energy contribution	-26.82
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-1.68
Structure conservation index	0.86
SVM decision value	1.33
SVM RNA-class probability	0.942374
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17139157 90 + 23771897
CUGGCUGAGGCUACUCAAGCCCGGCAUGGAGACAUUUAAGACGACUAUGUCGCCACCCCGUCAACGACGUCGAGUCCACCUCGAGUUGUG
..(((((((....))).))))(((..(((.(((((...........))))).)))..)))...(((((.(((((.....)))))))))). ( -32.30)
>DroSec_CAF1 23636 90 + 1
CUGGCUGAGGCUACUCAAGCCCGGCAUGGAGACAUUUAAGACGACUAUGUCGCCACCCCGUCAACGACGUCGAGUCCACCUCGAGUUGUG
..(((((((....))).))))(((..(((.(((((...........))))).)))..)))...(((((.(((((.....)))))))))). ( -32.30)
>DroEre_CAF1 24368 90 + 1
CUGGCUGAGGCUACUCAAGCCUGGCAUGGAGACAUUUAAGACGACUAUGUCGCCACCCCGUCAACGACGUCGAGUCCACCUCGAGUUGUG
..(((((((....))).))))(((((((....)))....(((......)))))))........(((((.(((((.....)))))))))). ( -31.60)
>DroYak_CAF1 25841 90 + 1
CUGGCUGAGGCUACUCAAGCCUGGCAUGGAGACAUUCAAGACGACUAUGUCGCCACCCCGUCAACGACGUCGAGUCCACCUCGAGUUGUG
..(((((((....))).))))(((((((....)))....(((......)))))))........(((((.(((((.....)))))))))). ( -31.60)
>DroAna_CAF1 5484 90 + 1
CUUUCGGUGGCUACUCAAGCCCGGCAUGGACACAUUCAAGACGACCAUGUCGCCACCCCAUCAACAUUUUCGAGUCCACCUCGAGUUGUG
.....((((((..(....)...(((((((...............)))))))))))))......(((..((((((.....)))))).))). ( -25.46)
>consensus
CUGGCUGAGGCUACUCAAGCCCGGCAUGGAGACAUUUAAGACGACUAUGUCGCCACCCCGUCAACGACGUCGAGUCCACCUCGAGUUGUG
.((((...((((.....)))).((((((....)))....(((......)))))).....))))(((((.(((((.....)))))))))). (-26.34 = -26.82 +   0.48)

alignment

secondary structure

dotplot

Window 2

Location	17,139,157 – 17,139,247
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	93.78
Mean single sequence MFE	-32.66
Consensus MFE	-28.28
Energy contribution	-28.52
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.23
Structure conservation index	0.87
SVM decision value	0.09
SVM RNA-class probability	0.579609
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17139157 90 - 23771897
CACAACUCGAGGUGGACUCGACGUCGUUGACGGGGUGGCGACAUAGUCGUCUUAAAUGUCUCCAUGCCGGGCUUGAGUAGCCUCAGCCAG
..(((((((((.....)))))....)))).(((.((((.(((((...........))))).)))).)))((((.(((....))))))).. ( -34.50)
>DroSec_CAF1 23636 90 - 1
CACAACUCGAGGUGGACUCGACGUCGUUGACGGGGUGGCGACAUAGUCGUCUUAAAUGUCUCCAUGCCGGGCUUGAGUAGCCUCAGCCAG
..(((((((((.....)))))....)))).(((.((((.(((((...........))))).)))).)))((((.(((....))))))).. ( -34.50)
>DroEre_CAF1 24368 90 - 1
CACAACUCGAGGUGGACUCGACGUCGUUGACGGGGUGGCGACAUAGUCGUCUUAAAUGUCUCCAUGCCAGGCUUGAGUAGCCUCAGCCAG
........(((((..((((((.((((....)((.((((.(((((...........))))).)))).)).))))))))).)))))...... ( -32.50)
>DroYak_CAF1 25841 90 - 1
CACAACUCGAGGUGGACUCGACGUCGUUGACGGGGUGGCGACAUAGUCGUCUUGAAUGUCUCCAUGCCAGGCUUGAGUAGCCUCAGCCAG
........(((((..((((((.((((....)((.((((.(((((..((.....))))))).)))).)).))))))))).)))))...... ( -32.70)
>DroAna_CAF1 5484 90 - 1
CACAACUCGAGGUGGACUCGAAAAUGUUGAUGGGGUGGCGACAUGGUCGUCUUGAAUGUGUCCAUGCCGGGCUUGAGUAGCCACCGAAAG
(((((((((((.....)))))....)))).)).(((((((.(((((.((.(......))).))))).)..((....)).))))))..... ( -29.10)
>consensus
CACAACUCGAGGUGGACUCGACGUCGUUGACGGGGUGGCGACAUAGUCGUCUUAAAUGUCUCCAUGCCGGGCUUGAGUAGCCUCAGCCAG
..(((((((((.....)))))....))))..((.((((.(((((...........))))).)))).))(((((.....)))))....... (-28.28 = -28.52 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:30 2006