Locus 713

Sequence ID	3R_DroMel_CAF1
Location	2,525,279 – 2,525,404
Length	125
Max. P	0.807323

overview

Window 8

Location	2,525,279 – 2,525,370
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	98.90
Mean single sequence MFE	-14.12
Consensus MFE	-13.60
Energy contribution	-13.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.38
Structure conservation index	0.96
SVM decision value	0.64
SVM RNA-class probability	0.807323
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2525279 91 - 27905053
UUUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCAAAAAAAGAGAA
....((((..(((....(((((((....)))))))..(((((..((....)).))))).........)))..))))............... ( -13.60)
>DroSec_CAF1 54642 91 - 1
UCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCAAAAAAAGCGAA
....((((..(((....(((((((....)))))))..(((((..((....)).))))).........)))..))))............... ( -13.60)
>DroSim_CAF1 53583 91 - 1
UCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCAAAAAAAGCGAA
....((((..(((....(((((((....)))))))..(((((..((....)).))))).........)))..))))............... ( -13.60)
>DroEre_CAF1 54381 91 - 1
UCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCAAAAAAAGAGAA
((((((((..(((....(((((((....)))))))..(((((..((....)).))))).........)))..))))..........)))). ( -14.90)
>DroYak_CAF1 55911 91 - 1
UCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCAAAAAAAGAGAA
((((((((..(((....(((((((....)))))))..(((((..((....)).))))).........)))..))))..........)))). ( -14.90)
>consensus
UCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCAAAAAAAGAGAA
....((((..(((....(((((((....)))))))..(((((..((....)).))))).........)))..))))............... (-13.60 = -13.60 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	2,525,290 – 2,525,404
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	97.98
Mean single sequence MFE	-15.80
Consensus MFE	-15.80
Energy contribution	-15.80
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.20
Structure conservation index	1.00
SVM decision value	0.46
SVM RNA-class probability	0.746555
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2525290 114 - 27905053
CACCACCCAUCCAUCCAUCACCCACCAAACGUCGUUUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCA
..((....................(((((.((((...))))..)))))......((((((((((((......))))))))))))......................))...... ( -15.80)
>DroSec_CAF1 54653 114 - 1
CACCACCCAUCCAUCCAUCACCCACCAAACGUCGUCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCA
..((....................(((((.((((...))))..)))))......((((((((((((......))))))))))))......................))...... ( -15.80)
>DroSim_CAF1 53594 114 - 1
CACCACCCAUCCAUCCAUCACCCACCAAACGUCGUCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCA
..((....................(((((.((((...))))..)))))......((((((((((((......))))))))))))......................))...... ( -15.80)
>DroEre_CAF1 54392 110 - 1
CACCAC----CCAUCCAUCACCCACCAAACGUCGUCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCA
..((..----..............(((((.((((...))))..)))))......((((((((((((......))))))))))))......................))...... ( -15.80)
>DroYak_CAF1 55922 114 - 1
CACCACCCACCCAUCCAUCACCCACCAAACGUCGUCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCA
..((....................(((((.((((...))))..)))))......((((((((((((......))))))))))))......................))...... ( -15.80)
>consensus
CACCACCCAUCCAUCCAUCACCCACCAAACGUCGUCUCGGCCCUUUGGACAAAAUUUACAUUUGAGUUUAAGUUUAGGUGUAAACAAUAAACAAAAAACAACAAUAGGCUACCA
..((....................(((((.((((...))))..)))))......((((((((((((......))))))))))))......................))...... (-15.80 = -15.80 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:02 2006