The four tick boxes allow you to select those parts of the sequence that can be removed. By default the program will remove domains as identified by SMART and Pfam and will leave only one copy of homologous regions found in the sequence. The users can optinally also add a filter to remove other globular regions predicted by GlobPlot. It is also possible to stop the filtering process or alter what things are filtered. We would, however, recommend caution when doing this as results can be either unpredictable, or motifs can be found that have no be aring on a common function, arising solely because long homologous stretches are found in the sequences.