Mapping to repetitive regions

[JueFish]

Anyone have any opinions on the best way to map to repetitive regions. In this case, we are mapping 454 reads from a specific chromosome where we have amplified a specific repetitive motif; howver, there is a di-nucleotide region often associate with these regions. To add to the problem, we are using mouse as a reference, but are doing this in another rodent, so gaps are kind of an issue. Currently, I'm using bwa and playing with the gap penalties to see if it improves my % mapping for reads. I have thought of using blast/blat as well as there aren't a ton of reads so it's do-able. Thought it might be able to handle the gaps better. Any other thoughts? I'd be curious if anyone had any opinions on mappers and their relative ability to handle these kinds of issues with indels.

Thanks.

Nate