Sequence Dot Plot
While sequence alignments allow for visualization of individual matching nucleotides, it can mask some larger-scale features of DNA or RNA sequences, including repeats and inversions. Dot plots show sequence alignments on a two-dimensional plot, where one sequence is placed on the X axis, and the other on the Y axis. Analysis occurs by aligning a portion of the sequence based on window size (default is analysis every 10 bases), and if the mismatches are at or below the limit (default limit is 0), the tool will place a dot at the aligned X and Y coordinates. This allows for each set of 10 bases to be independently compared against the query sequence, highlighting more complex relationships. For instance, reverse complements can be visualized as green dots and repeats appear as multiple stacked diagonal lines. Dot plots are often used to identify regions with direct or inverted repeats, frameshifts, inversions, and low complexity within a sequence by aligning it against itself.
Note: Increasing window size and mismatch limit can reduce stringency to reveal more divergent relationships, but this will increase background noise.