DAF format for a list of lists of pairs

The following file contains only the compulsory (bold) and recommended elements of a valid DAF format for presenting an aligned pair. Note the following:

• Keywords are mandatory (ALISYM, NPAIRS, NSEARCH, idSeq, idStr, lenSeq, lenStr, seq, str).
• Lines starting with # and no keyword will be ignored.
• Columns are separated by tabs or blanks.
• For a simple rank analysis you can skip the sequences.

'seq' = sequence of search sequence U,

'str' = sequence of database protein.

# DAF (dirty alignment format for exchange with Aqua)
# ALISYM	ACDEFGHIKLMNPQRSTVWY.acdefghiklmnpqrstvwy
# NSEARCH	2
# NPAIRS	3,2		(NOTE: the commata separate different search sequences, i.e. U1, U2, ..)
# ALIGNMENTS