Locus 1949

Sequence ID 3R_DroMel_CAF1
Location 5,500,797 – 5,500,917
Length 120
Max. P 0.662957
window3203

overview

Window 3

Location 5,500,797 – 5,500,917
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.14
Mean single sequence MFE -16.94
Consensus MFE -0.34
Energy contribution -0.58
Covariance contribution 0.24
Combinations/Pair 1.25
Mean z-score -1.43
Structure conservation index 0.02
SVM decision value 0.27
SVM RNA-class probability 0.662957
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5500797 120 + 27905053
UCCACCUGUUAACUACCUGUUAUCCACCUGUUAACUAAAUGGAUACACCUGUUAACCACCAAACCAACAAACAUUGUAAACAAACUCCAUGUUACCAAGGCAACAUAGCUAAGAUGUUAA
.......((((((....(((.(((((...(....)....))))))))...)))))).............((((((...((((.......)))).....(((......)))..)))))).. ( -16.10)
>DroSec_CAF1 429 109 + 1
ACCACCUGUUAUCCACCUGUUA-----------ACCACCUGGAUACACCUGUUGGCCACCAAAGCAACAAGCACUGUAAACCAACUCCAUAUUACCAACGCAACAUAGCUUAGAUGUUAA
......(((.(((((..((...-----------..))..))))))))...(((((....((..((.....))..))....)))))....................((((......)))). ( -14.60)
>DroSim_CAF1 429 109 + 1
UCCACCUGUUAACUACCUGUUA-----------ACCACCUGGAUACACUUGUUGGCCACCAAAGCAACAAGCACUGUAAACAAACUUCAUAUUACCAACGCAACAUAGCUUAGAUGUUAA
((((...((((((.....))))-----------))....))))(((((((((((..........)))))))...))))...........................((((......)))). ( -17.70)
>DroEre_CAF1 422 106 + 1
GCCACCUGUUAUCCACCAGUUA-----------GGUACCUGA-AACACCUGA-AACCACCAACCCAACAAACACUUCAAACAAACUCCAUAUUACCAAGGAAACAUAACUUGGAGGU-AA
(((.((.(((((.......(((-----------(((......-...))))))-.............................................(....))))))..)).)))-.. ( -14.50)
>DroYak_CAF1 398 107 + 1
ACCACCUGUAAACCACCUGCUG-----------AGUACCUGGUUACAGCUGA-AACCAGCAGUCCUACAAACAGU-GAAACAAACUGCGUAUUACCAAGGCAACAUAGCUUAGAAGUUUA
........(((((.....((((-----------.((.(((((((((.((((.-...))))...........((((-.......)))).)))..))).)))..)).))))......))))) ( -21.80)
>consensus
ACCACCUGUUAACCACCUGUUA___________ACUACCUGGAUACACCUGUUAACCACCAAACCAACAAACACUGUAAACAAACUCCAUAUUACCAAGGCAACAUAGCUUAGAUGUUAA
.........................................................................................................((((......)))). ( -0.34 =  -0.58 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:38 2006