[Arabidopsis] Searching the Whole Arabidopsis Genome for a Motif

[Siobhan A. Braybrook]

Dear All,

I am trying to search the whole Arabidopsis genome for a short DNA 
sequence, to obtain the genomic co-coordinates for every instance.
I want to search everything, regardless of classification as gene, 
intergenic, upstream, etc.
And I would like to get back Chromomsonal nucleotide positions, not 
positions relative to an AGI locus number.

Any ideas?

I have tried several approaches at TAIR with some problems:
The only way to search the whole genome is via the BAC clones.
PatMatch gives you positions relative to AGI loci.

Any help is appreciated!

Siobhan Braybrook

S. A. Braybrook
Graduate Student, Harada Lab
Section of Plant Biology
University of California,  Davis
Davis, CA 95616
Ph 530.752.6980

The time is always right, to do what is right.
- Martin Luther King, Jr.