This program masks a glam2 motif out of sequences, so that weaker motifs can be found. Masking replaces residues aligned to key positions with the symbol 'x'. By alternately applying glam2 and glam2mask several times, it is possible to find the strongest, second-strongest, third-strongest, etc. motifs in a set of sequences.
glam2mask -o mask1.fa my_motif.glam2 my_seqs.fa
glam2mask -x n my_motif.glam2 my_seqs.fa
If the sequences do not have unique names, glam2mask may mask the wrong ones. It also assumes that the order of the sequences does not change, so don't do that.