Quick Tips: White X's in the directed dot plot indicate true palindromes the same size as your window size. You can use the mouse to drag the plot in any directions. Just click the left mouse button and drag. I find that dragging works best in IE 9.0 and Chrome and as of this writing performs the worst in Firefox. The images are constructed from line segments. The more lines, then the slower the dragging performance. Low scoring matches are colored in blue with low contrast to the black background.
A directed dot plot is like a standard dot plot for comparing two sequences. One sequence lies along the horizontal axis at the top of the plot and the second lies along the left vertical axis. Rather than plotting a single point when two words match, in a directed dot plot a diagonal is drawn. The length of the diagonal corresponds to the number of matching characters.
There are two possible directions for a diagonal. One is a forward diagonal angled at 45 degrees from the top left to bottom right. The other is a reverse diagonal angled at 45 degrees from the bottom left to top right. For a forward diagonal words in sliding windows along both axes are compared in their normal forward direction. For a reverse diagonal, the word from the horizontal sequence is compared to the reverse of the word from the vertical sequence.
The default is to compare words of length 5 with mismatches. The default number of mismatches is 2. In the forward direction, diagonals are colored red for 3 or more matches and blue otherwise. In the reverse direction, diagonals are colored yellow for 3 or more matches and blue otherwise. All points are plotted on a black background.
The theory in perception is that the brain responds preattentively to the visual cues of line length, line direction, and line color. Patterns consisting of these visual cues are immediately noticed. Our brains are wired to find these patterns almost instantly. By constructing a flow matrix using small line segments where matches occur rather than single points, we are able to instantly recognize many interesting patterns where sequences match.