For FASTA3, the maximum data length is set in the file defs.h, by
MAXTST and MAXLIB. The maximum practical length is about MAXTST,
15000. However, your query sequence can initially be up to
MAXTST+MAXLIB (15000+60000) and then you can select a subsequence, for
Since FASTA currently reports only the once match from a query sequence,
it is dangerous to give it too long a query sequence, as some lower scoring
matches may be missed.