The flexible pattern is defined around the block_file format described in APPENDIX II. The only additions necessary are if flexible gaps are to be included, when the following syntax is used.
>test this is a test flexible pattern >test2 this is also a flexible pattern *iteration 1 ag each line in this file vl <23:28 defines a pattern "ELEMENT" pg ww <1:3 kr . . further pattern elements here . etc *
This file means: score against ag at position 1, vl at position 2 then allow between 23 and 28 gaps (inclusive) then score against pg, then ww, then allow a gap of 1 to 3 residues, then score kr etc etc.