Locus 5500

Sequence ID	X_DroMel_CAF1
Location	14,268,408 – 14,268,503
Length	95
Max. P	0.801493

overview

Window 3

Location	14,268,408 – 14,268,503
Length	95
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	89.87
Mean single sequence MFE	-29.82
Consensus MFE	-23.02
Energy contribution	-23.30
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.83
Structure conservation index	0.77
SVM decision value	0.62
SVM RNA-class probability	0.801493
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14268408 95 + 22224390
G-------GCUAGAAUGUAGCAAAGGAAAGCAGGAAAAGAAAGAACGAAGGCGAGUCCUUGCAGGUGAUUUCCGUUUGUCGCCAGCGGCAACUUAGCUGUCA
(-------(((((..(((.((.(((((..((.(............)....))...)))))...((((((........)))))).)).)))..)))))).... ( -25.80)
>DroSec_CAF1 9048 95 + 1
G-------GCUAGAAAGUAGCGAAGGAAAGGAGGAAAAGAAAGGACGAAGCCGAGUCCUUGCAGGUGAUUUCCGUUUGUCGCCAGCGGCAACUUAGCUGUCA
(-------((((...(((.((...................((((((........))))))((.((((((........)))))).)).)).)))))))).... ( -26.80)
>DroSim_CAF1 13048 95 + 1
G-------GCUAGAAAGUAGCGAAGGAAAGCAGGAAAAGAAAGGACGAAGGCGAGUCCUUGCAGGUGAUUUCCGUUUGUCGCCAGCGGCAACUUAGCUGUCA
.-------((((.....))))....((.((((((......((((((........))))))((.((((((........)))))).)).....))).))).)). ( -27.20)
>DroEre_CAF1 11824 97 + 1
-----GAAGCGCGAAAGCGGCGAAGGAAAGCGGGAAAAGAAAGGACGAAGGCGAGUCCUUGCAGGUGAUUUCCGUUUGUCGCCAGCGGCAACUUGGCUGUCA
-----.....((....))(((((....(((((((((..(.((((((........)))))).....)..))))))))).))))).(((((......))))).. ( -37.30)
>DroYak_CAF1 12285 102 + 1
GGCGAGAAAGGAGAAAGUAACGAAGGAAGGCAGGAAAAGAAAGGACGAAGGCGAGUCCUUGCAGGUGAUUUCCGUUUGUCGCCAGCGGCAACUUAGCUGUCA
(((((.((((((((..((..(....)...)).......(.((((((........)))))).)......))))).))).))))).(((((......))))).. ( -32.00)
>consensus
G_______GCUAGAAAGUAGCGAAGGAAAGCAGGAAAAGAAAGGACGAAGGCGAGUCCUUGCAGGUGAUUUCCGUUUGUCGCCAGCGGCAACUUAGCUGUCA
................(((((.(((....((.........((((((........))))))((.((((((........)))))).)).))..))).)))).). (-23.02 = -23.30 +   0.28)

alignment

secondary structure

dotplot

Window 4

Location	14,268,408 – 14,268,503
Length	95
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	89.87
Mean single sequence MFE	-22.62
Consensus MFE	-19.64
Energy contribution	-19.88
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.35
Structure conservation index	0.87
SVM decision value	0.28
SVM RNA-class probability	0.665840
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14268408 95 - 22224390
UGACAGCUAAGUUGCCGCUGGCGACAAACGGAAAUCACCUGCAAGGACUCGCCUUCGUUCUUUCUUUUCCUGCUUUCCUUUGCUACAUUCUAGC-------C
.((.(((...((((((...))))))....(((((......((((((.....)))).)).......))))).))).))....((((.....))))-------. ( -22.12)
>DroSec_CAF1 9048 95 - 1
UGACAGCUAAGUUGCCGCUGGCGACAAACGGAAAUCACCUGCAAGGACUCGGCUUCGUCCUUUCUUUUCCUCCUUUCCUUCGCUACUUUCUAGC-------C
.....((((.((((((...))))))....(((((......(.((((((........)))))).).)))))....................))))-------. ( -22.00)
>DroSim_CAF1 13048 95 - 1
UGACAGCUAAGUUGCCGCUGGCGACAAACGGAAAUCACCUGCAAGGACUCGCCUUCGUCCUUUCUUUUCCUGCUUUCCUUCGCUACUUUCUAGC-------C
.((.(((...((((((...))))))....(((((......(.((((((........)))))).).))))).))).))....((((.....))))-------. ( -24.50)
>DroEre_CAF1 11824 97 - 1
UGACAGCCAAGUUGCCGCUGGCGACAAACGGAAAUCACCUGCAAGGACUCGCCUUCGUCCUUUCUUUUCCCGCUUUCCUUCGCCGCUUUCGCGCUUC-----
.((.(((...((((((...))))))....(((((......(.((((((........)))))).).))))).))).))....((.((....))))...----- ( -24.20)
>DroYak_CAF1 12285 102 - 1
UGACAGCUAAGUUGCCGCUGGCGACAAACGGAAAUCACCUGCAAGGACUCGCCUUCGUCCUUUCUUUUCCUGCCUUCCUUCGUUACUUUCUCCUUUCUCGCC
((((......((((((...))))))....(((((......(.((((((........)))))).).)))))...........))))................. ( -20.30)
>consensus
UGACAGCUAAGUUGCCGCUGGCGACAAACGGAAAUCACCUGCAAGGACUCGCCUUCGUCCUUUCUUUUCCUGCUUUCCUUCGCUACUUUCUAGC_______C
.((.(((...((((((...))))))....(((((......(.((((((........)))))).).))))).))).))......................... (-19.64 = -19.88 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:27 2006