I was trying to align two full chromosome sequences (one contig for each chromosome) with Mummer v3.1, and I get mummer dot plot to visualize the alignment. These two chromosomes were actually very similar, however, the aligned region (red dots) were not shown on the diagonal. I am wondering is there a parameter I should change to let mummer put all the aligned region on the diagonal or I need to do some other manipulations on my sequence file (fasta files).

The commands I used for this alignment was:

nucmer --maxgap=500 --mincluster=100 --prefix=ref_qry ref.fa qry.fa
show-coords -r ref_qry.delta > ref_qry.coords
show-aligns ref_qry.delta "ref" "qry" > ref_qry.aligns
delta-filter -q -r ref_qry.delta > ref_qry.filter
mummerplot --postscript ref_qry.filter -R ref.fa -Q qry.fa

Thank you for your help!