T. This follows the Genbank convention. N and X represent any letter and remain unchanged. With -e, this will trace the upper envelope. Most programs compare the sequence in file1 with the sequence in file2 . 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. Also, profile programs use alpha and beta as deletion scores for the sequence being searched. The first line of a profile contains its name. Indel substrings are penalized by a score of alpha for the first letter, and by beta for subsequent letters in the indel. The examples below illustrate the application of scoring parameters to evaluate alignments.