Locus 5824

Sequence ID	3L_DroMel_CAF1
Location	15,750,571 – 15,750,724
Length	153
Max. P	0.974105

overview

Window 1

Location	15,750,571 – 15,750,684
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.28
Mean single sequence MFE	-40.48
Consensus MFE	-37.60
Energy contribution	-37.23
Covariance contribution	-0.37
Combinations/Pair	1.06
Mean z-score	-2.41
Structure conservation index	0.93
SVM decision value	1.72
SVM RNA-class probability	0.974105
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15750571 113 + 23771897
UUGGGCCACCCACUUGGGCAUU-------UGGCAUUGUCCUUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGACCACAAAAGGGGGCAGACAUUAAAUUAGUCGAAGGCCGAGGCCA
...((((.(((....)))...(-------((((....((..(((((((((......((((..(((((....)))))..)))))))))))))(((.........)))))..))))))))). ( -40.60)
>DroSec_CAF1 2269 113 + 1
UUGGGCCACCCACUUGGGCAUU-------UGGCAUUGUCCUUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGACCACAAAAGGGGGCAGACAUUAAAUUAGUCGAAGGCCGAGGCCA
...((((.(((....)))...(-------((((....((..(((((((((......((((..(((((....)))))..)))))))))))))(((.........)))))..))))))))). ( -40.60)
>DroSim_CAF1 2500 113 + 1
UUGGGCCACCCACUCGGGCAUU-------UGGCAUUGUCCUUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGACCACAAAAGGGGGCAGACAUUAAAUUAGUCGAAGGCCGAGGCCA
...((((.(((....)))...(-------((((....((..(((((((((......((((..(((((....)))))..)))))))))))))(((.........)))))..))))))))). ( -40.30)
>DroEre_CAF1 2252 119 + 1
UUGGGCCACCCACUUGGGCAUUUGGCAUUUGGCAUUGUCCUUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGGCCACAAAAAGGGGCAGACAUUAAAUUAGUCGAAGG-CGAGGCCA
....(((((((....)))....))))...((((.(((.((((((((((((......((((..(((((....)))))..)))))))))))).(((.........))).))))-))).)))) ( -40.40)
>consensus
UUGGGCCACCCACUUGGGCAUU_______UGGCAUUGUCCUUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGACCACAAAAGGGGGCAGACAUUAAAUUAGUCGAAGGCCGAGGCCA
...((((.(((....)))................(((.((((((((((((......((((..(((((....)))))..)))))))))))).(((.........))).)))).))))))). (-37.60 = -37.23 +  -0.37)

alignment

secondary structure

dotplot

Window 2

Location	15,750,571 – 15,750,684
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.28
Mean single sequence MFE	-35.88
Consensus MFE	-33.46
Energy contribution	-33.52
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.93
SVM decision value	0.84
SVM RNA-class probability	0.863434
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15750571 113 - 23771897
UGGCCUCGGCCUUCGACUAAUUUAAUGUCUGCCCCCUUUUGUGGUCGCACAAUUGCGAAAACAAUAUGUCAAAAGGGCAAGGACAAUGCCA-------AAUGCCCAAGUGGGUGGCCCAA
.(((....)))...(((.........))).((((((..((((..(((((....)))))..))))..........(((((.((......)).-------..)))))....))).))).... ( -36.80)
>DroSec_CAF1 2269 113 - 1
UGGCCUCGGCCUUCGACUAAUUUAAUGUCUGCCCCCUUUUGUGGUCGCACAAUUGCGAAAACAAUAUGUCAAAAGGGCAAGGACAAUGCCA-------AAUGCCCAAGUGGGUGGCCCAA
.(((....)))...(((.........))).((((((..((((..(((((....)))))..))))..........(((((.((......)).-------..)))))....))).))).... ( -36.80)
>DroSim_CAF1 2500 113 - 1
UGGCCUCGGCCUUCGACUAAUUUAAUGUCUGCCCCCUUUUGUGGUCGCACAAUUGCGAAAACAAUAUGUCAAAAGGGCAAGGACAAUGCCA-------AAUGCCCGAGUGGGUGGCCCAA
.(((....)))...(((.........))).((((((..((((..(((((....)))))..))))..........(((((.((......)).-------..)))))....))).))).... ( -36.80)
>DroEre_CAF1 2252 119 - 1
UGGCCUCG-CCUUCGACUAAUUUAAUGUCUGCCCCUUUUUGUGGCCGCACAAUUGCGAAAACAAUAUGUCAAAAGGGCAAGGACAAUGCCAAAUGCCAAAUGCCCAAGUGGGUGGCCCAA
.((((...-.....(((.........))).(((((((.((((...((((....))))...))))..........(((((.((.((........))))...)))))))).))))))))... ( -33.10)
>consensus
UGGCCUCGGCCUUCGACUAAUUUAAUGUCUGCCCCCUUUUGUGGUCGCACAAUUGCGAAAACAAUAUGUCAAAAGGGCAAGGACAAUGCCA_______AAUGCCCAAGUGGGUGGCCCAA
.((((....................(((((...((((((((((.(((((....)))))...))......))))))))...)))))................((((....))))))))... (-33.46 = -33.52 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	15,750,604 – 15,750,724
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-32.41
Consensus MFE	-30.99
Energy contribution	-31.05
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.18
Structure conservation index	0.96
SVM decision value	1.10
SVM RNA-class probability	0.914398
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15750604 120 + 23771897
UUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGACCACAAAAGGGGGCAGACAUUAAAUUAGUCGAAGGCCGAGGCCAUCAAACUGUCCAAAAUACACAUAAAUUCAAUCGGGGAAAA
((.(((..((((....((((..(((((....)))))..))))....((((((((.........)))((.(((....))).))....)))))...............))))..))).)).. ( -32.90)
>DroSec_CAF1 2302 120 + 1
UUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGACCACAAAAGGGGGCAGACAUUAAAUUAGUCGAAGGCCGAGGCCAUCAAACUGUCCAAAAUACACAUAAAUUCAAUCGGGGAAAA
((.(((..((((....((((..(((((....)))))..))))....((((((((.........)))((.(((....))).))....)))))...............))))..))).)).. ( -32.90)
>DroSim_CAF1 2533 120 + 1
UUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGACCACAAAAGGGGGCAGACAUUAAAUUAGUCGAAGGCCGAGGCCAUCAAACUGUCCAAAAUACACAUAAAUUCAAUCGGGGAAAA
((.(((..((((....((((..(((((....)))))..))))....((((((((.........)))((.(((....))).))....)))))...............))))..))).)).. ( -32.90)
>DroEre_CAF1 2292 119 + 1
UUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGGCCACAAAAAGGGGCAGACAUUAAAUUAGUCGAAGG-CGAGGCCAUCGAGCUGUCCAAAAUACACAUAAAUUCAAUCGGGGAAUA
((.(((..((((....((((..(((((....)))))..))))....((((((............((((.((-(...))).)))).))))))...............))))..))).)).. ( -30.92)
>consensus
UUGCCCUUUUGACAUAUUGUUUUCGCAAUUGUGCGACCACAAAAGGGGGCAGACAUUAAAUUAGUCGAAGGCCGAGGCCAUCAAACUGUCCAAAAUACACAUAAAUUCAAUCGGGGAAAA
((.(((..((((....((((..(((((....)))))..))))....((((((((.........)))((.(((....))).))....)))))...............))))..))).)).. (-30.99 = -31.05 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:59 2006