args << "scan_for_matches"
args << "-c" if options[:comp]
args << "-p" if options[:seq_type] == :protein
- args << "-o" if options[:overlap]
+ args << "-o 1" if options[:overlap]
args << "-n #{options[:max_misses]}" if options[:max_misses]
args << "-m #{options[:max_hits]}" if options[:max_hits]
args << File.join(@tmp_dir, "#{i}.pat")