AqmcR2.chr1.chr2.fish.bed - this files contain genome coordinates of putative region for fish in chr1 
AqmcR2.chr1.chr2.fish.fa - this files contain sequences of putative region for fish in chr1 
For example, we will make probe to distinguish 3L1 and 3L2 chromosome haplotypes.
To make probe on _3L1_:
1) AqmcR2.12.full.agp AqmcR2.12.full.contig.breaks.bed -- to define of contigs that you will test
2) AqmcR2.3L1.3L2.fish.bed   -- to find "good" locus in tested contigs
3) AqmcR2.3L1.3L2.fish.fa    -- to define of nucleotide sequence of choosen "good" locus

To make probe on _3L2_:
1) AqmcR2.12.full.agp AqmcR2.12.full.contig.breaks.bed -- to define of contigs that you will test
2) AqmcR2.3L2.3L1.fish.bed   -- to find "good" locus in tested contigs
3) AqmcR2.3L2.3L1.fish.fa    -- to define of nucleotide sequence of choosen "good" locus