When padding the target region to create the design region, the design region should be padded by the complete max amplicon length. It is currently padded by half this length, which artificially constrains the search space. e.g., for a max amplicon length of 400 bp, it would be valid to have one primer situated 300 bp to the left of the target and one primer situated 50 bp to the right of the target. However, if we only consider the 200 bp flanking either side of the target, this pair would not be considered as a valid design.
Per discussion with Tim and Erin today
When padding the target region to create the design region, the design region should be padded by the complete max amplicon length. It is currently padded by half this length, which artificially constrains the search space. e.g., for a max amplicon length of 400 bp, it would be valid to have one primer situated 300 bp to the left of the target and one primer situated 50 bp to the right of the target. However, if we only consider the 200 bp flanking either side of the target, this pair would not be considered as a valid design.