Locus 1563

Sequence ID	X_DroMel_CAF1
Location	4,469,594 – 4,469,713
Length	119
Max. P	0.633289

overview

Window 1

Location	4,469,594 – 4,469,713
Length	119
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	96.08
Mean single sequence MFE	-43.27
Consensus MFE	-38.14
Energy contribution	-38.03
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.80
Structure conservation index	0.88
SVM decision value	-0.03
SVM RNA-class probability	0.520638
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4469594 119 + 22224390
CCUCAAAGAAGUGGCCAGUUCACCGUUCAAGGAUGAGUCCCAGGACCUGGUUCCAGUGGCCAAGCUGGUGGACAAUGCCACCAGCCAGAACAUGGGCUUCAACAGCUAUUUCCGGCCCA
..........(..(((((.(((((......)).)))(((....))))))))..).(.((((..((((((((......))))))))..(((....((((.....))))..))).))))). ( -42.80)
>DroSec_CAF1 71236 119 + 1
CCUCAAAGAAGUGGCCAGUUCGCCGUUCAAGGAUGAGUCCCAGGACCUGGUUCCAGUGGCCAAGCUGGUGGACAAUGCCACCAGCCAGAACAUGGGCUUCAACAGCUAUUUCCGGCCCA
..........(.((((.(((((((((((..(((....)))..))))(((....))).)))...((((((((......))))))))..))))...((((.....))))......))))). ( -44.50)
>DroYak_CAF1 72097 119 + 1
CCUCAAAGAAGUGGCCAGUUCGCCGUUCAAGGAUGAGUCGCAGGACCUGGUGCCGGUGUCCAAGCUGGUGGACAAUGCCACCAGCCAGAACAUGGGCUUCAACAGCUAUUUUCGACCCA
.......(((((..(((((((((..((((....))))..)).(((((((....))).))))..((((((((......))))))))..)))).))))))))................... ( -42.50)
>consensus
CCUCAAAGAAGUGGCCAGUUCGCCGUUCAAGGAUGAGUCCCAGGACCUGGUUCCAGUGGCCAAGCUGGUGGACAAUGCCACCAGCCAGAACAUGGGCUUCAACAGCUAUUUCCGGCCCA
.......((((((((.......((......)).((((.((((((.((((....))).).))..((((((((......)))))))).......)))).))))...))))))))....... (-38.14 = -38.03 +  -0.11)

alignment

secondary structure

dotplot

Window 2

Location	4,469,594 – 4,469,713
Length	119
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	96.08
Mean single sequence MFE	-47.17
Consensus MFE	-43.01
Energy contribution	-42.90
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.82
Structure conservation index	0.91
SVM decision value	0.21
SVM RNA-class probability	0.633289
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4469594 119 - 22224390
UGGGCCGGAAAUAGCUGUUGAAGCCCAUGUUCUGGCUGGUGGCAUUGUCCACCAGCUUGGCCACUGGAACCAGGUCCUGGGACUCAUCCUUGAACGGUGAACUGGCCACUUCUUUGAGG
..((((((.....((((((.(((.(((((..(.(((((((((......))))))))).)..)).))).....((((....))))....))).))))))...))))))............ ( -47.10)
>DroSec_CAF1 71236 119 - 1
UGGGCCGGAAAUAGCUGUUGAAGCCCAUGUUCUGGCUGGUGGCAUUGUCCACCAGCUUGGCCACUGGAACCAGGUCCUGGGACUCAUCCUUGAACGGCGAACUGGCCACUUCUUUGAGG
..((((((.....((((((.(((.(((((..(.(((((((((......))))))))).)..)).))).....((((....))))....))).))))))...))))))............ ( -48.70)
>DroYak_CAF1 72097 119 - 1
UGGGUCGAAAAUAGCUGUUGAAGCCCAUGUUCUGGCUGGUGGCAUUGUCCACCAGCUUGGACACCGGCACCAGGUCCUGCGACUCAUCCUUGAACGGCGAACUGGCCACUUCUUUGAGG
(((((((.....(.(((.....(((..(((((.(((((((((......))))))))).)))))..)))..))).)....))))))).(((..((.(((......))).....))..))) ( -45.70)
>consensus
UGGGCCGGAAAUAGCUGUUGAAGCCCAUGUUCUGGCUGGUGGCAUUGUCCACCAGCUUGGCCACUGGAACCAGGUCCUGGGACUCAUCCUUGAACGGCGAACUGGCCACUUCUUUGAGG
..((((((.....((((((.(((((..((.((.(((((((((......))))))))).)).))..)).....((((....))))....))).))))))...))))))............ (-43.01 = -42.90 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:38 2006