Geneious Prime
Geneious Biologics
Repeat Finder
Find large, distant repeats
Requires Geneious 9.0+
A plugin to Identify regions in one or more sequences that are repeated elsewhere in the sequences and then visualize the results as an annotation heatmap. Capable of identifying perfect and near-perfect repeats.
Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting a nucleotide sequence and choosing Annotate & Predict - Find Repeats from the menu. Results are saved as annotations on your sequence.