Locus 2960

Sequence ID X_DroMel_CAF1
Location 7,901,474 – 7,901,593
Length 119
Max. P 0.522968
window4856

overview

Window 6

Location 7,901,474 – 7,901,593
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.76
Mean single sequence MFE -18.09
Consensus MFE -12.79
Energy contribution -13.42
Covariance contribution 0.63
Combinations/Pair 1.09
Mean z-score -1.65
Structure conservation index 0.71
SVM decision value -0.02
SVM RNA-class probability 0.522968
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7901474 119 + 22224390
GUGGGUUACAUAAACAAAAAAUAAAUAAUG-AGGCCCACAAACAAACAGAUAGAAACGAAAAUAACAAUCACAAUGUACCACUAAAAGUGCGGCGGUUGCCAUAAACAAUAUGCGACACC
((((((..(((................)))-..))))))................................(..(((((........)))))..)(((((.(((.....))))))))... ( -20.09)
>DroSec_CAF1 2095 115 + 1
GUGGGUUACAUAAACAAAAAAUAAAUAAUG-AUGCCCACAA----ACAGAUAAAAACGAAACUAACAAUCAAAAUGUACCACUAAAAGUGCGGCGGUUGCCAUAAACAAUAUGCGACACC
((((((..(((................)))-..))))))..----.............................(((((........)))))...(((((.(((.....))))))))... ( -17.99)
>DroSim_CAF1 5208 116 + 1
GUGGAUUACAUAAACAAAAAAUAAAUAAUGGAUGCCCACAA----ACAGAUAAAAACGAAACUAAUUAUCAAAAUGUACCACUAAAAGUGCGGCGGUUGCCAUAAACAAUAUGCGACACC
((((..(((((.................(((....)))...----...(((((............)))))...))))))))).........((..(((((.(((.....)))))))).)) ( -16.60)
>DroYak_CAF1 5236 117 + 1
UAGGGUUACAUAAACAAAAAAUAAAUAAUG-GGGCCCACAAACAAACAGACAGAAACGAAACUAACAAUUACAAUCU--CGCUAAAAGUGCGGCAGUUGCCAUAAACAAUAUGCGACACC
..((((..(((................)))-..)))).......................................(--(((.......))))..(((((.(((.....))))))))... ( -17.69)
>consensus
GUGGGUUACAUAAACAAAAAAUAAAUAAUG_AGGCCCACAA____ACAGAUAAAAACGAAACUAACAAUCAAAAUGUACCACUAAAAGUGCGGCGGUUGCCAUAAACAAUAUGCGACACC
((((((..(((................)))...))))))...................................(((..(((.....)))..)))(((((.(((.....))))))))... (-12.79 = -13.42 +   0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:45 2006