Methods and kits to determine the presence of exogenous alleles within a native haplotype are provided. Introduction of foreign alleles into livestock genomes has provided the ability to introduce specific desirable traits. The present disclosure provides methods to identify the presence of exogenous alleles that foreign to a haplotype at a target locus, and identify specific markers that are native to the haplotype. Identification of exogenous genes at a target locus, flanked by native markers is indicative that the exogenous gene is present through molecular engineering. Conversely, the presence of an exogenous gene that are only partially flanked by native markers is indicative that the allele is present due to sexual breeding.