fragrep is a free and open-source tool for detecting nucleotide pattern fragments in genomes that occur in a given order. A tolerance can be specified separately for each pattern.
The goal of fragrep is to detect distant homologous sequences that exhibit a commonly observed fragmented conservation pattern.
Furthermore, fragrep provides a set of other tools, most notably aln2pattern for extracting homology patterns from multiple sequence alignments as well as visualization of the homology patterns.
Detailed instructions on how to use the fragrep utility on your Mac are available HERE.
fragrep is cross-platform and it works on Mac OS X and Linux. Binaries for the Linux platform are available on the project's homepage.