Check the advice in the How can I align my 454 reads to a reference sequence and generate a recruitment plot, basically the author recommends that you;

have a look at this paper http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050077 basically you would want to BLASTn you reads against a reference genome. then, parse the BLAST results to extract the hits' coordinates and percent ID