ABSTRACT
Figure 2 (Figure 5 in Leese & Held). Dotplots of four microsatellite-containing contigs against themselves (Geneious Pro version 5.3). The main diagonal indicates the perfect identity of the sequence (X axis) against itself (Y axis). Off-diagonal parallels to the main diagonal indicate that sequence motifs occur elsewhere in the sequence, albeit slightly modified and thus not easily detected using bioinformatic approaches or inspection by eye. Candidate sequences with enough room to place primers in unique parts of the flanking sequence (indicated by lack of parallels, upper left panel) are to be preferred over candidates with cryptically repetitive flanking regions. Note that the Phobos search for repeats with commonly used parameters only identifies one additional 8 bp repeat (annotations in lower panel; Geneious Pro). The remaining repeat structures are camouflaged by their lower degree of sequence conservation in the sequence view (lower panel), but clearly visible in the dotplot of the same sequence (lower left panel).
