Dotter is a graphical dotplot program for detailed comparison of two sequences.
Here, every residue in one sequence is compared to every residue in the other
sequence. The first sequence runs along the x-axis and the second sequence
along the y-axis. In regions where the two sequences are similar to each other,
a row of high scores will run diagonally across the dot matrix. If you're
comparing a sequence against itself to find internal repeats, you'll notice
that the main diagonal scores maximally, since it's the 100% perfect
self-match.

To make the score matrix more intelligible, the pairwise scores are averaged
over a sliding window which runs diagonally. The averaged score matrix forms a
three-dimensional landscape, with the two sequences in two dimensions and the
height of the peaks in the third. This landscape is projected onto two
dimensions by aid of greyscales - the darker grey of a peak, the higher it is.

Dotter provides a tool to explore the visual appearance of this landscape, as
well as a tool to examine the sequence alignment it represents.

WWW: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html