Self microsynteny

[manoharbisht1998]

First of all, thank you very much for this complete toolkit.

I have performed the MCScanX analysis for intraspecies synteny, and I want to plot the microsynteny within the genome. Let's say I have a gene on chromosome 12 which has syntenic gene pairs in chr 6. How should I approach this through JCVI? Can I use the MCScanx intraspecific collinearity file?

PS: I have already tried keeping the copy of the same genome features with changed gene ids, but I didn't work the way I wanted.

Thanks
Manohar