biopython-motifs , How can I create motif from sequences of different length?
Motifs are not designed to be variable length in general since PSSMs/PVMs don't support insertions/deletions (indels). Instead, I suggest profile HMMs, such as those offered by HMMER3, which do support indels. You can parse HMMER3 output with Biopython via Bio.SearchIO.HmmerIO