Hi I have done pan-genome analysis with 0.5% identity cutoff using BPGA tool. and it has given me core reference sequence, accessory reference file and unique sequences files. Now I have a list of sequence and i have aligned them with all 3 files i.e core, accessory and unique. There are some genes that shows alignment with core genome as well as accessory genome sequences. My parameters are >=50% identity, qcovhsp >=90% and evalue 0.0001. How can I segregate genes in core and accessory if they shows alignment with both files?