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Not all pairs of alleles will have the same phenotype: dominance when AA = Aa in phenotype, A is dominant, a is recessive. An allele can be dominant over one allele but recessive to another allele.
Genes Have Alleles. The traits an organism displays are ultimately determined by the genes it inherited from its parents, in other words by its genotype. Animals have two copies of all their chromosomes, one from each parent.