Locus 10197

Sequence ID 3R_DroMel_CAF1
Location 27,363,048 – 27,363,155
Length 107
Max. P 0.500000
window16238

overview

Window 8

Location 27,363,048 – 27,363,155
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 73.42
Mean single sequence MFE -21.34
Consensus MFE -10.06
Energy contribution -11.38
Covariance contribution 1.31
Combinations/Pair 1.21
Mean z-score -1.99
Structure conservation index 0.47
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27363048 107 - 27905053
AAAA--UUACAGAGGGCAAAAUUGUAAGAUCUACUUAAUUUAGAUUUUCAGGAUCCGUUCAAAAAUAAACUUA-----------ACUGAAUUUUUUGAGUGCCUCUGUAAAAUAUAGUCA
....--(((((((((.((...(((.((((((((.......)))))))))))......((((((((........-----------.......))))))))))))))))))).......... ( -23.66)
>DroSec_CAF1 108520 109 - 1
AAGAGGUUACAGAGGGCAAAAUUGUAAGAUCUACUAAAUUUAGAUUUUCAGGAUCCGCUCAAAAAUAUACUAA-----------AUUGAAUUUUUCGAGUGCCUCUGUAAAAUAUAGUCA
......(((((((((......(((.((((((((.......)))))))))))....(((((((((((.((....-----------..)).)))))).)))))))))))))).......... ( -25.90)
>DroSim_CAF1 72717 102 - 1
-------UACAGAGGGCAAAAUUGUAAGAUCUACUAAAUUUCGAUUUUCAGGAUCCGCUCAAAAAUAUACUAA-----------AUCGAAUAUUUCGCGUGCCUCUGUAAAAUAUAGUCA
-------((((((((.((.........(((((...((((....))))...)))))(((....((((((.(...-----------...).)))))).)))))))))))))........... ( -20.40)
>DroEre_CAF1 73031 104 - 1
UUAU--UUAUGAAAGGCCAAAUUUUA--------------CAGAUUUCCAAGGUCCUCUCAAAAUCAUACUAAAUAAUUACACUAUUGACUUUUUCGAGUGCCCCUGUGAAAUAUAGUCA
....--........(((...((((((--------------(((........((..(((..(((((((...................))).))))..)))..)).)))))))))...))). ( -15.41)
>consensus
AAAA__UUACAGAGGGCAAAAUUGUAAGAUCUACUAAAUUUAGAUUUUCAGGAUCCGCUCAAAAAUAUACUAA___________AUUGAAUUUUUCGAGUGCCUCUGUAAAAUAUAGUCA
......(((((((((...........................((((.....))))(((((((((((.......................)))))).)))))))))))))).......... (-10.06 = -11.38 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:11 2006