The scoring parameters are all integer values, and all positive. The first line is the sequence name, and should be used as a description.
Subsequent lines contain the sequence to be used.
The sequences themselves may contain blanks, returns, and other whitespace for readability. Only multiple sequences in the first file will be processed. Smith, T.F., M.S. Waterman, and W.M. Fitch. Comparative biosequence metrics. Maps , sequences and genomes .