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The Dotplot plugin provides a tool to build dot plots dotplots for DNA or RNA sequences. This allows comparing these sequences graphically. Using a dot plotdotplot, 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 dot plotsdotplots, navigation in a dot plotdotplot, dot plots dotplots synchronization, saving and loading a dot plotdotplot, etc.

An example of a dot plot dotplot view:

     <img src="/wiki/download/attachments/4227416/Dotplot.png"/>

The Dotplot plugin uses the Repeat Finder plugin to build a dot plotdotplot, make sure you have the Repeat Finder plugin installed.