# Dot plot comparisons
Structural comparison of two assemblies to reveal rearrangements or repeats.
**To start:** pick a **query** and **reference** genome. Search by name or upload a FASTA/GenBank file for each.
[Guide →](https://docs.abrinca.com/arx/guides/dotplot/)
Display & settings
(click to toggle)
Plot size
Alignments
Sequence labels
Grid lines
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Click and drag to zoom in, double-click to zoom out, Ctrl+scroll to zoom with the mouse wheel.
Gene annotations appear as arrows along scaffold tracks (visible when zoomed in): ► forward strand, ► reverse strand.
Click a scaffold track to isolate it; click again to reset.