I am trying to extract a gene marker, say, COII (cytochrome oxidase subunit II) (e.g., NCBI: JQ319797), from a sequenced but unassembled insect genome, Musca domestica (house fly) (NCBI: AQPM00000000). I downloaded all the scaffolds, created a local BLAST database, and blastned a COII homolog against this database. The result includes multiple hits, each looking like a real COII, but they slightly differ from each other in sequence. I thought one genome should only contain one version of gene, but the result seems to be a mixture. I am asking if it is an artifact due to the imcompleteness of the genome sequencing project, or I did something wrong, or, since it is a mitochondrial gene, there are supposed to be different versions within an insect? And how should I correctly get this gene marker from the genome? Thank you!