SLiMMaker is a simple tool for generating regular expression motifs from aligned peptide sequences. It was originally made for making new SLiM definitions based on a set of aligned occurrences and therefore the ends of these peptides are typically not the actual ends of sequences. Sometimes, however, such as in the KDEL ER retrieval motif, they are at (or near) the end (or beginning) of a protein and you might want that taken into consideration when generating a motif.
The SLiMMaker website will now accept beginning (^) and end ($) of seuqence characters. The peptides still need to be aligned, so if using them you should fill in any non-conforming peptides with an X. If the peptides are of different lengths and the end of lines character ends up appearing within an ambiguous position with regular amino acids (e.g. [$AGS]), SLiMMaker will truncate the regular expression at that point (not including that position) - otherwise it just gets too messy!
This upgrade will appear in the next distributions of SLiMSuite and SeqSuite. As always, if it is not clear then just try it out with some test sequences. (And report any odd behaviour.)