With/without unscaffolded contigs has different alignment results

[justdx]

I am using Minimap2 to map two Arabidopsis assemblies. However, I found that the same chromosome pair (chr5) aligned differently when I align the Ragtag outputs directly (including unscaffolded contigs) or when I only align 5 chromosome-level scaffolds. I think this is a tandem repeat region, but I don't know what is the cause and are there any parameters that would allow me to find the most reliable alignment?