The Dotplot plugin provides a tool to build dotplots for DNA or RNA sequences. This allows comparing these sequences graphically. Using a dotplot, you can easily identify such differences between sequences as mutations, inversions, insertions, deletions and low-complexity regions.
Also the plugin provides advanced features: comparing multiple dotplots, navigation in a dotplot, dotplots synchronization, saving and loading a dotplot, etc.
An example of a dotplot view:
The Dotplot plugin uses the Repeat Finder plugin to build a dotplot, make sure you have the Repeat Finder plugin installed.
The Dotplot features are described in more details below.