Reciprocity of matching regions

[ckeeling]

Hello,

I notice that I don't get similar results from ref=reference.fa fa=scaffolds.fa as I do with ref=scaffolds.fa fa=reference.fa. I am looking at one sequence in reference.fa, and 4 sequences in scaffolds.fa. All sequences are greater than the default m=100000, and they do all have matching regions. Sum of scaffold lengths approximately equal to size of reference_1.

jupiter ng=200 name=ref_scaff ref=ref.fa fa=scaff.fa
cat ref_scaff.seqOrder.txt
ref0	reference_1	scaf2	scaffold_2	-
ref0	reference_1	scaf4	scaffold_4	+
ref0	reference_1	scaf1	scaffold_1	+
ref0	reference_1	scaf3	scaffold_3	-

jupiter ng=200 name=scaff_ref ref= scaff.fa fa=ref.fa
cat scaff_ref.seqOrder.txt
ref0	scaffold_1	scaf1	reference_1	+

Is this expected behaviour? Thanks, Chris