DNA Parameters

Two sets of substitution scores and gap penalties are used, one for DNA and cDNA sequences, and the other for protein sequences. If both sequences are DNA or cDNA sequences, then the values in the top parameter panel are used by the alignment programs. In this case, the score for each match is always 10, and the user can change the score for each mismatch (a negative integer), the gap open penalty (a non-negative integer), and the gap extension penalty (a positive integer).