• Motif Width (MEME)
  This is the width (number of characters in the sequence pattern) of a single motif. MEME chooses the optimal width of each motif individually using a statistical heuristic function. You can choose different limits for the minimum and maximum motif widths that MEME will consider. The width of each motif that MEME reports will lie within the limits you choose.
  Note on maximum width:
  Both protein and DNA motifs are often shorter than the default "maximum width" (50). It is often advisable for you to reduce that parameter to a much smaller value (e.g., in the range 10--20) by entering a new value in the box.
• Number of aligned columns (GLAM2)
  GLAM2 allows you to set limits on the number of "key positions"-- the aligned columns--in motifs. (Because GLAM2 allows gaps, instances of the motif may not have the same width as the number of aligned columns.) GLAM2 automatically adjusts the number of key positions so as to maximize the alignment score, but it sometimes has trouble with this. You can help GLAM2 by changing the initial number of aligned columns to a ballpark value. You can also set lower and upper bounds on the number of aligned columns in the motif.
  Note on maximum number of aligned columns:
  Both protein and DNA motifs are often shorter than the default "maximum number of aligned columns" (50). It is often advisable for you to reduce that parameter to a much smaller value (e.g., in the range 10--20) by entering a new value in the box.