Figure 1: 

Principle of the 3-frame nested translation dotmatrix comparison. The X-axis shows the 3-frame nested translation, the Y-axis a standard protein sequence. Colored squares show identity matches between the X and Y axis, a different color is used for each frame. The dotted diagonal line indicates the diagonal that would become even more apparent at smaller scale, when appropriate stringency and window settings were chosen.

Figure 2:

Screen shot of the main window of PPCMatrix. At the left the loaded sequences are selectable in the scrollbox. Different features of the main window are indicated in the figure.