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.