-- a gap in linear scoring global alignments Gap -4 -- gap opening in affine languages GapOpen -4 -- gap extension in affine languages GapExtend -2 -- opening the prefix or suffix in overhang languages PreSufOpen -1 -- extending the prefix or suffix in overhang languages PreSufExtend 0 -- score to return for bigram mismatches Mismatch -3 -- needs to be set, but is not used (need better simple scoring parser) Match -999999