When plotting:
./dotplot.py --fasta 1.fa 2.fa --gui
and
./dotplot.py --fasta 1.fa 2.fa --window_size 10 --gui
in both cases we really consider all residues/nucleotides etc, so full sequence should be shown in both cases. In the second case, the sequence is trimmed to the dimensions of plotted matrix, which shouldn't be the case.