Locus 490

Sequence ID	X_DroMel_CAF1
Location	1,418,932 – 1,419,026
Length	94
Max. P	0.740683

overview

Window 4

Location	1,418,932 – 1,419,026
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	89.15
Mean single sequence MFE	-17.19
Consensus MFE	-13.65
Energy contribution	-13.89
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.40
Structure conservation index	0.79
SVM decision value	-0.02
SVM RNA-class probability	0.525692
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1418932 94 + 22224390
AUUGCUUUCAAAACAACCAUGCACAGCAACCCACACACACGCACACGUCCAAUAAUACGGCCACUGAGACAAGGACCCAAGUCCUUGGUCUUUG
.(((((..((.........))...)))))................(((........)))......(((((((((((....)))))).))))).. ( -15.00)
>DroSec_CAF1 25355 94 + 1
AUUGCUCUCAAAACAACCAUGCACAGCAACCCACACACACGCACACGUCCAAUAAUACGGCCACUGAGCCAAGGACCCAAGUCCUUGGUCUUUG
.(((((..((.........))...)))))................(((........)))......(((((((((((....)))))))).))).. ( -17.10)
>DroSim_CAF1 15978 94 + 1
AUUGCUCUCAAAACAACCAUGCACAGCAACCCACACACACGCACACGUCCAAUAAUACGGCCACUGAGCCAAGGACCCAAGUCCUUGGUCUUUG
.(((((..((.........))...)))))................(((........)))......(((((((((((....)))))))).))).. ( -17.10)
>DroEre_CAF1 20669 80 + 1
AUUGCUCUCAAAACAACCACGCAC--------------ACGCAUACGUCCAAUAAUAUGGCCACUGAGCCAAGGACCCAAGUCCUUGGUCUUUG
......((((..........((..--------------..))....(.(((......))).)..))))((((((((....))))))))...... ( -18.60)
>DroYak_CAF1 17006 94 + 1
AUUGCUCUCAAAACAACCAUGCACACACACAGACGCAUACGCACACGUCCAAUAAUAUGGCCACUGAGGCAAGGACCCAAGUCCUUGGUCUUUG
..(((...............)))....((.((((((....))....(.(((......))).).......(((((((....))))))))))).)) ( -18.16)
>consensus
AUUGCUCUCAAAACAACCAUGCACAGCAACCCACACACACGCACACGUCCAAUAAUACGGCCACUGAGCCAAGGACCCAAGUCCUUGGUCUUUG
......((((..........((..................))....(.((........)).)..))))((((((((....))))))))...... (-13.65 = -13.89 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	1,418,932 – 1,419,026
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	89.15
Mean single sequence MFE	-29.52
Consensus MFE	-23.15
Energy contribution	-23.64
Covariance contribution	0.49
Combinations/Pair	1.16
Mean z-score	-1.67
Structure conservation index	0.78
SVM decision value	0.45
SVM RNA-class probability	0.740683
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1418932 94 - 22224390
CAAAGACCAAGGACUUGGGUCCUUGUCUCAGUGGCCGUAUUAUUGGACGUGUGCGUGUGUGUGGGUUGCUGUGCAUGGUUGUUUUGAAAGCAAU
((((((((((((((....)))))(((..(((..(((.(((...((.(((....))).)).))))))..))).))))))))..))))........ ( -28.20)
>DroSec_CAF1 25355 94 - 1
CAAAGACCAAGGACUUGGGUCCUUGGCUCAGUGGCCGUAUUAUUGGACGUGUGCGUGUGUGUGGGUUGCUGUGCAUGGUUGUUUUGAGAGCAAU
.......(((((((....)))))))((.(((..(((.(((...((.(((....))).)).))))))..))).))...(((((((...))))))) ( -31.90)
>DroSim_CAF1 15978 94 - 1
CAAAGACCAAGGACUUGGGUCCUUGGCUCAGUGGCCGUAUUAUUGGACGUGUGCGUGUGUGUGGGUUGCUGUGCAUGGUUGUUUUGAGAGCAAU
.......(((((((....)))))))((.(((..(((.(((...((.(((....))).)).))))))..))).))...(((((((...))))))) ( -31.90)
>DroEre_CAF1 20669 80 - 1
CAAAGACCAAGGACUUGGGUCCUUGGCUCAGUGGCCAUAUUAUUGGACGUAUGCGU--------------GUGCGUGGUUGUUUUGAGAGCAAU
((..((((((((((....)))))))).))..)).(((......)))((((((....--------------)))))).(((((((...))))))) ( -26.00)
>DroYak_CAF1 17006 94 - 1
CAAAGACCAAGGACUUGGGUCCUUGCCUCAGUGGCCAUAUUAUUGGACGUGUGCGUAUGCGUCUGUGUGUGUGCAUGGUUGUUUUGAGAGCAAU
........((((((....))))))(((((((..(((((......((((((((....))))))))((......)))))))..)..)))).))... ( -29.60)
>consensus
CAAAGACCAAGGACUUGGGUCCUUGGCUCAGUGGCCGUAUUAUUGGACGUGUGCGUGUGUGUGGGUUGCUGUGCAUGGUUGUUUUGAGAGCAAU
......((((((((....))))))))(((((..(((((........(((....)))..(((..(....)..))))))))..)..))))...... (-23.15 = -23.64 +   0.49)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:50 2006