fragrep: Homology Search with Fragmented Nucleic Acid Sequence Patterns
fragrep implements an efficient algorithm for detecting nucleotide pattern fragments in genomes that occur in a given order. For each pattern a tolerance can be specified separately.
available under the GNU GPL,
fragrep uses some postscript sources of the WebLogo package, which is subject to the MIT Open Source License.
aln2pattern, and a sample fasta sequence for testing the resulting pattern.