You can use Biostring in Bioconductor.

The function countPattern should do the job. Just check if it is using a sliding window or not.

Jellyfish is pretty nice for kmer counting.

I wrote a simple script for finding patterns (regular expressions in fact) in fasta files, it's fastaRegexFinder.py and I also happen to mention it in this post Quadruplex sequence batch prediction

If you just want to count the number of occurrences you can do

fastaRegexFinder.py -f genome.fa -r 'ACTTTAG' | wc -l

You can also use bowtie1.

It is specially nice in finding (mapping) short sequences..