Locus 4750

Sequence ID	2L_DroMel_CAF1
Location	13,570,886 – 13,571,046
Length	160
Max. P	0.979390

overview

Window 3

Location	13,570,886 – 13,571,006
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.00
Mean single sequence MFE	-29.40
Consensus MFE	-27.00
Energy contribution	-26.68
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-1.19
Structure conservation index	0.92
SVM decision value	0.09
SVM RNA-class probability	0.578843
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13570886 120 + 22407834
GGCGUAGGAGAACUCGUUUGCCCAAAUGAGUCAUAAACACUGAGGAGGCCAAAAACGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACUACAUUUGAACU
...((((((..((((((((((((...(.(((.......))).).).)))...)))))))).))...(((((....)))))...(((((........)))))......))))......... ( -30.20)
>DroSec_CAF1 4200 120 + 1
AGCGUAGGAUAACUUGUUUGCCCAAAUGAGUCAUAAACACUGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACAACAUUUGAACU
.((((..((((.(((((((((((...(.(((.......))).).).)))...)))))))))))..)))).((.((((......(((((........)))))........)))).)).... ( -26.34)
>DroSim_CAF1 3747 120 + 1
AGCGUAGGAUAACUCGUUUGCCCAAAUGAGUCAUAAACACUGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACAACAUUUGAACU
.((((..((((.(((((((((((...(.(((.......))).).).)))...)))))))))))..)))).((.((((......(((((........)))))........)))).)).... ( -28.44)
>DroEre_CAF1 4662 120 + 1
AGCGUCGGAGAACUCGUUUGCCCAAAUGAGUCAUAAACACUGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAGCACGAUUGGGAUGAACCAAACUACAUUUGAACU
.((((..((..((((((((((((...(.(((.......))).).).)))...)))))))).))..)))).....(((((.......))))).((((......)))).............. ( -30.10)
>DroYak_CAF1 713 120 + 1
AGUGUAGGAGAACUCGUUUGCCCAAAUGAGUCAUAAACACUGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACUACAUUUGAACU
(((((((((..((((((((((((...(.(((.......))).).).)))...)))))))).))...(((((....)))))...(((((........)))))......)))))))...... ( -31.90)
>consensus
AGCGUAGGAGAACUCGUUUGCCCAAAUGAGUCAUAAACACUGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACUACAUUUGAACU
...........((((((((((((...(.(((.......))).).).)))...)))))))).((((((((((....)))).............((((......)))).....))))))... (-27.00 = -26.68 +  -0.32)

alignment

secondary structure

dotplot

Window 4

Location	13,570,926 – 13,571,046
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-32.26
Consensus MFE	-29.22
Energy contribution	-31.16
Covariance contribution	1.94
Combinations/Pair	1.09
Mean z-score	-1.75
Structure conservation index	0.91
SVM decision value	1.84
SVM RNA-class probability	0.979390
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13570926 120 + 22407834
UGAGGAGGCCAAAAACGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACUACAUUUGAACUUGAAAAAGUUUUCGCCGAAAUUCGUUUUUCGUCUGCAAGC
...(.((((.((((((((((.((...(((((....))))).........(((((((......)))).........((((((....)))))))))..)).)))))))))).)))).).... ( -34.70)
>DroSec_CAF1 4240 120 + 1
UGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACAACAUUUGAACUUGAAAAAGUUUUCGCCGAAAUUCGUUUUUCGUUUGCAAGC
...(.((((.((((((((((.((...(((((....))))).........(((((((......)))).........((((((....)))))))))..)).)))))))))).)))).).... ( -32.20)
>DroSim_CAF1 3787 120 + 1
UGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACAACAUUUGAACUUGAAAAAGUUUUCGCCGAAAUUCGUUUUUCGUCUGCAAGC
...(.((((.((((((((((.((...(((((....))))).........(((((((......)))).........((((((....)))))))))..)).)))))))))).)))).).... ( -34.70)
>DroEre_CAF1 4702 120 + 1
UGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAGCACGAUUGGGAUGAACCAAACUACAUUUGAACUUGAAAAAGUUUUCGCCGCAAUUUGUUUUCCGUCUGCAAGC
...((((..((((.(((.((((((((((......(((((.......))))).((((......))))....)))))))((((....))))...))))))..))))..)))).......... ( -31.60)
>DroYak_CAF1 753 120 + 1
UGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACUACAUUUGAACUUGAAAAAGUUUUCGCCAAAAUGUGUUUUCCGUCUGCAAGC
...(.((((..(((((..(((.....(((((....))))).......)))..((((......))))...((((((((((((....))))))......)))))))))))..)))).).... ( -28.10)
>consensus
UGAGGAGGCCAAAAGCGAGUGUCAAAUGCACACAUGUGCACCAUCAUCACGAUUGGGAUGAACCAAACUACAUUUGAACUUGAAAAAGUUUUCGCCGAAAUUCGUUUUUCGUCUGCAAGC
...(.((((.((((((((((.((...(((((....))))).........(((((((......)))).........((((((....)))))))))..)).)))))))))).)))).).... (-29.22 = -31.16 +   1.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:17 2006