Locus 1810

Sequence ID	3R_DroMel_CAF1
Location	5,167,655 – 5,167,777
Length	122
Max. P	0.998333

overview

Window 1

Location	5,167,655 – 5,167,757
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	97.25
Mean single sequence MFE	-28.84
Consensus MFE	-27.82
Energy contribution	-27.82
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.96
SVM decision value	3.07
SVM RNA-class probability	0.998333
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5167655 102 - 27905053
AGAGAGGGAGGGGAGCGCGGAAAAGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGCUGACGAUGACAGUUGUGGGUAAUUGAAGCCAA
.....((((((....(((......)))....))))(((((((((((((((((((.....)))))))))))).(((((....)))))))))))).....)).. ( -28.30)
>DroSec_CAF1 6227 102 - 1
AGAGAGGGAGGGGAGCGCGGAAAAGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGCUGACGAUUACAGUUGUGGGUAAUUGAAGCCAA
(((....((((....(((......)))....))))....)))....((((((((.....))))))))((((..(((((((........))))))).)))).. ( -30.00)
>DroSim_CAF1 6172 102 - 1
AGAGAGGGAGGGGAGCGCGGAAAAGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGCUGACGAUGACAGUUGUGGGUAAUUGAAGCCAA
.....((((((....(((......)))....))))(((((((((((((((((((.....)))))))))))).(((((....)))))))))))).....)).. ( -28.30)
>DroEre_CAF1 5966 102 - 1
AGAGAGGGAGGGGAGCGCGGGGUUGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGCUGACGAUGACAGUUGUGGGUAAUUGAAGCCAA
....................((((.(((((((((.......(((((((((((((.....)))))))))))))(((((....)))))))))))))).)))).. ( -28.80)
>DroYak_CAF1 6350 102 - 1
AGAGAGGGAGGGGAGCGCGGGGUUGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGCUGACGAUGACAGUUGUGGGUAAUUGAAGCCAA
....................((((.(((((((((.......(((((((((((((.....)))))))))))))(((((....)))))))))))))).)))).. ( -28.80)
>consensus
AGAGAGGGAGGGGAGCGCGGAAAAGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGCUGACGAUGACAGUUGUGGGUAAUUGAAGCCAA
.....((((((....(((......)))....))))(((((((((((((((((((.....)))))))))))).(((((....)))))))))))).....)).. (-27.82 = -27.82 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	5,167,687 – 5,167,777
Length	90
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	95.81
Mean single sequence MFE	-26.96
Consensus MFE	-25.38
Energy contribution	-25.14
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-1.22
Structure conservation index	0.94
SVM decision value	0.57
SVM RNA-class probability	0.785644
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5167687 90 - 27905053
AGCGCACUAACACGACCGA--GAGAGAGGGAGGGGAGCGCGGAAAAGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGC
.((((.((....(..((..--......))..).)).))))...(((((....)))))........(((((((((((.....))))))))))) ( -26.50)
>DroSec_CAF1 6259 90 - 1
GGCGCACUAACACGACCGA--GAGAGAGGGAGGGGAGCGCGGAAAAGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGC
.((((.((....(..((..--......))..).)).))))...(((((....)))))........(((((((((((.....))))))))))) ( -26.30)
>DroSim_CAF1 6204 90 - 1
GGCGCACUAACACGACCGA--GAGAGAGGGAGGGGAGCGCGGAAAAGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGC
.((((.((....(..((..--......))..).)).))))...(((((....)))))........(((((((((((.....))))))))))) ( -26.30)
>DroEre_CAF1 5998 90 - 1
GGCGCACUAACACGACCGA--GAGAGAGGGAGGGGAGCGCGGGGUUGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGC
.((((.((....(..((..--......))..).)).)))).((((.((((.....)))).)))).(((((((((((.....))))))))))) ( -28.20)
>DroYak_CAF1 6382 92 - 1
AGCGCACUAACACGACCGAAAGAGAGAGGGAGGGGAGCGCGGGGUUGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGC
.((((.((....(..((..........))..).)).)))).((((.((((.....)))).)))).(((((((((((.....))))))))))) ( -27.50)
>consensus
GGCGCACUAACACGACCGA__GAGAGAGGGAGGGGAGCGCGGAAAAGUGAUUACUUUAUUAUCUAGUUUAGUUAGCAAGGCGCUGACUGGGC
.((((.((....(..((..........))..).)).))))(((...((((.....))))..))).(((((((((((.....))))))))))) (-25.38 = -25.14 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:06 2006