Maybe try different ploidy levels, smdugeplot, or if you have enough compute k=55

"What do you mean I can't run this insanely inefficient program without interruption for 21 days?"

If the dot plot looks the same it's probably a long tandem duplicate, at least 3 copies. Check read coverage in this area also to see if it's real or possibly an assembly error

"I think we don't think often enough about their work because it's easy not to celebrate the folks who are protecting you from that which doesn't appear because of the work that they're doing"
- Senator Warnock

Be sure to check out the "Application of Genetics and Genomics for Large-scale Breeding Programs" session organized by Samantha McConaughy and myself Monday at 12:50pm.