contig mapping reference blat psl result handle

[Jane Lee]

I mapped my resequencing contigs to the reference which is the same species with blat to locate these contigs, than I want to join the ordered contigs into big ones according to their position on the reference to run gene prediction, do anyone have the experience to do this and a tested script can finish this? And I found that two different contigs overlap on the same tens of basepairs on the reference, is this normal?

Thank you in advance!

Best wishes!