This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. This sets the alternate display of matches and mismatches in alignments. Output file format The output from matcher is a sequence alignment.
Users can provide their own data files in their own directories.
Diagnostic Error Messages None. Exit status 0 upon successful completion. Known bugs None. Finds all exact matches of a given size between 2 sequences water will give a single best rigorous local alignment. It will use memory of the order of the product of the lengths of the sequences to be aligned.