Links within the same sequence

[Artifice120]

Afternoon,

Thanks for making such a flexible program.
While Mapping TIR's within contigs I realized it may be useful to also visualize the links between them as a sort of "center".
My question is, is there a way to make the links feature be drawn for links within the same sequence ?

what I have so far

[thackl]

Do you mean you want to draw some sort of connector between the TIRs on the same contig? Something like:

TIR------------RIT
 |______________|

[Artifice120]

Yes, exactly.
The contact map shows each chromosome has a central loop sticking out and it would be helpful to see that visualized in the IR's as well.