Attached to this email are the deliverables for a probe selection that allows for up to 5 matches. You will see that the coverage has not substantially improved. I once again believe that this is because the presence of all the N bases in the P.microlepis.txt target region file.
You’ll see that the match5 design covers 44.2 / 61.9% (0 bp and 100 bp offset, respectively). As an academic exercise, I allowed for 100 matches in the genome and saw that the 100 match design covers 44.9 / 62.9% (0 bp and 100 bp offset, respectively). Therefore, there’s not much more that we can do with the current design given the quality of the starting sequence.
Please let me know how you would like to proceed.
