This in silico protocol allows to have an insight into the sequence divergence of selected genomic region, including missing information, gaps and allignment with Open Reading Frames. The protocol is written for model plant Arabidopsis thaliana, but can be possibly adapted to plotting the divergence of any organism, for which multiple accessions were resequenced. We used this script to produce divergence plots in our paperMagdalena M. Julkowska, Karlijn Klei, Like Fokkens, Michel A. Haring, M. Eric Schranz, Christa Testerink; Natural variation in rosette size under salt stress conditions corresponds to developmental differences between Arabidopsis accessions and allelic variation in theLRR-KISSgene,Journal of Experimental Botany, Volume 67, Issue 8, 1 April 2016, Pages 2127–2138,https://doi.org/10.1093/jxb/erw015