The example presented there may give one or two hints on how to use the algorithm and interpret some results. The sequence format is the fasta one. The alphabet filename contains a matrix used to specify if two letters match and what score must be used. Lines correspond to pattern alphabet letters.
Columns correspond to sequence alphabet letters.
Numbers are the score that is used when the two letters are aligned. Every letter of each alphabet must be in this file because sat use it to determine sequence and pattern alphabet.