(A) A single, contiguous gene homolog in a target genome with 100% query length coverage has an ECNC of 1.0. (B) Two contiguous gene homologs each with 100% query length coverage have an ECNC of 2.0. (C) A single gene homolog, split across multiple scaffolds and contigs in a fragmented target genome; BLAT identifies each fragment as a single hit. Per nucleotide of query sequence, there is only one corresponding nucleotide over all the hits, thus the ECNC is 1.0. (D) Two gene homologs, one fragmented and one contiguous. 100% of nucleotides in the query sequence are represented between all hits; however, every nucleotide in the query has two matching nucleotides in the target genome, thus the ECNC is 2.0. (E) One true gene homolog in the target genome, plus multiple hits of a conserved domain that span 20% of the query sequence. While 100% of the query sequence is represented in total, 20% of the nucleotides have four hits. Thus, the ECNC for this gene is 1.45. (F) Two real gene homologs; one hit is contiguous, one hit is fragmented in two, and the tail end of both sequences was not identified by BLAT due to sequence divergence. Only 75% of the query sequence was covered in total between the hits, but for that 75%, each nucleotide has two hits. As such, ECNC is equal to 2.0 for this gene.