Dear community,

I'm working with a genomic region with segmental duplication. I could see from the dot plot below (the region against itself) that there are 3 paralogous segments in the region. However, I was wondering if there are any good tools to identify each paralog and mark the breakpoints? Alternatively, a good "synteny finder" might also suffice: I could take this sequence and try to find synteny against itself. I tried to align the sequence to itself using minimap2, but minimaps2 only gives the diagonal of the dot plot since it's 100% sequence identity.

I would highly appreciate your advice!

Changxu