dottup looks for places where words (tuples) of a specified length have an exact match in both sequences and draws a diagonal line over the position of these words.

Here is a sample session with dottup:

% dottup embl:eclac embl:eclaci -wordsize=6 -gtitle="eclaci vs eclac"

Mandatory qualifiers (bold if not always prompted):

[-sequencea] (sequence)

Sequence USA.

[-sequenceb] (sequence)

Sequence USA.

-wordsize (integer)

Word size.

-data (boolean)

Output the match data to a file instead of plotting it.

-graph (graph)

Graph type.

-xygraph (xygraph)

Graph type.

-outfile (outfile)

Output filename.

Optional qualifiers (bold if not always prompted):

-[no]boxit (boolean)

Draw a box around dotplot.

Advanced qualifiers:

-stretch (boolean)

Use nonproportional axes.