dotdot · genomic dot plots

Data

reference

Target FASTA —

Query FASTA = target

Drop files anywhere. One FASTA → self plot; a second becomes the query; three or more — the first is the target, the rest stack on the query axis. The buttons multi-select. dotdot computes the plot itself — alignment-free, no aligner in the loop, chromosome scale included.

Aligner PAF —

Optional: load an aligner's PAF (minimap2 etc., .gz ok). With a plot already on screen it overlays the aligner's calls on the raw k-mer truth; on an empty app it plots standalone.

Matching

k-mer size

bridge gaps ≤

skip k-mers with >

min match length

sampling

Display

min identity off

min segment length

forward reverse

color by

line width 2

emphasize small matches

lock 1:1 bp aspect

Legend

no data

Plot

go to target region G

Hover

Drop FASTA files for an alignment-free dot plot
(or an aligner's PAF, to audit it) — try real data: or the