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+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