The two sequences are placed on the axes of a rectangular image and (in the simplest forms of dotplot) wherever there is a similarity between the sequences a dot is placed on the image.
Where the two sequences have substantial regions of similarity, many dots align to form diagonal lines. It is therefore possible to see at a glance where there are local regions of similarity as these will have long diagonal lines. It is also easy to see other features such as repeats (which form parallel diagonal lines), and insertions or deletions (which form breaks or discontinuities in the diagonal lines).
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. This is a fast, but not especially sensitive way of creating dotplots. It is an acceptable method for displaying regions of substantial similarity between two sequences.
Using a longer word (tuple) size displays less random noise, runs extremely quickly, but is less sensitive. Shorter word sizes are more sensitive to shorter or fragmentary regions of similarity, but also display more random points of similarity (noise) and runs slower.
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dotmatcher, by comparison, moves a window of specified length up each diagonal and displays a line over the window if the sum of the comparisons (using a substitution matrix) exceeds a threshold. It is slower but much more sensitive.