Locus 3968

Sequence ID X_DroMel_CAF1
Location 10,524,955 – 10,525,061
Length 106
Max. P 0.500000
window6523

overview

Window 3

Location 10,524,955 – 10,525,061
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 69.39
Mean single sequence MFE -33.98
Consensus MFE -6.50
Energy contribution -8.58
Covariance contribution 2.08
Combinations/Pair 1.07
Mean z-score -2.23
Structure conservation index 0.19
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10524955 106 + 22224390
GCCAAAGCACUUGGAAGGUAUAAUGGA-GCCACGCCCCCUUCUCGGGAGAA-----GGGC---ACUGCAGUUGA-AAGUCAAUUGCAG----UGAAACCUUAGCCCAGUUAUGAGAGCAA
......((.(((((((((.....((..-..)).....)))))).(((..((-----((.(---((((((((((.-....)))))))))----))...))))..)))......))).)).. ( -41.10)
>DroSec_CAF1 56291 109 + 1
ACCAAAGCACUUGAAGGGUAUAAUGAU-GCCACGCCCCUUUUGCAGGAGAA-----GGGCGGAACUGCAGUUGA-AAGUCAAUUGCAG----UGAAACCUUAGCCCAGUUAUGAGAGCAA
......((.(((...((((........-....(((((.((((....)))).-----)))))..((((((((((.-....)))))))))----).........))))......))).)).. ( -33.60)
>DroSim_CAF1 59888 109 + 1
GCCAAAGCACUUGAAAGGUAUAAUGGU-GCCACGCCCCUUUCGCAGGAGAA-----GGGCGGAACUGCAGUUGA-AAGUCAAUUGCAG----UGAAACCUUAGCCCAGUUAUGAGAGCAA
......((.(((((..((..(((.(((-..(.(((((.((((....)))).-----)))))..((((((((((.-....)))))))))----))..))))))..))..))..))).)).. ( -37.20)
>DroEre_CAF1 58222 92 + 1
CCCAUAGCACUUGGCAAGUAUAAUGGA-GCCACGCCCUUU-CUCACGAGGA---------------------GA-AGGCCAACUGCAG----UGAAACCUUAGCCCAGUUAUGAGAGCAA
..(((.(((.(((((.........((.-((...))))(((-(((.....))---------------------))-))))))).))).)----))........(((((....)).).)).. ( -22.60)
>DroYak_CAF1 58696 117 + 1
GCCAUAGCACUUGGGUAGUAUAAUGGAUGCCACGCCCCUU--UCGCGAAGGGAGGCGAGGGGCAGUGCAGUUGA-AAGGCAAUUGCAGUGAGUGAAACCUUAGCCCAGUUAUGAGAGCAA
((((((((...(((((.((((.....))))((((((((..--((((........)))))))))(.((((((((.-....)))))))).)..)))........)))))))))))...)).. ( -41.90)
>DroAna_CAF1 60580 91 + 1
-----------------AUAAAUUCUG-GUUAUGCCAAGUGGGCA--AAAG-----GGGC---GUGGCAGUGGCUGUGGCAAUGCCAGUUA-AGAAACCUUAGCCCAGUUAUGAGAGCAA
-----------------.....((((.-((..((((.....))))--....-----((((---.(((((...((....))..)))))..((-((....))))))))....)).))))... ( -27.50)
>consensus
GCCAAAGCACUUGGAAGGUAUAAUGGA_GCCACGCCCCUUUCGCAGGAGAA_____GGGC___ACUGCAGUUGA_AAGUCAAUUGCAG____UGAAACCUUAGCCCAGUUAUGAGAGCAA
.................................((.............................(((((((((......)))))))))..........((((.........)))).)).. ( -6.50 =  -8.58 +   2.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:08 2006