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Alleles are corresponding pairs of genes located at specific positions in the chromosomes. Together, alleles determine the genotype. Alleles which determine some aspect of the phenotype, the physical appearance of an organism, are said to be coding alleles.

When both alleles in a pair are the same, the alleles are homozygous. If the alleles are different, they are heterozygous. In the case of homozygous alleles, the expression of phenotype is usually very straightforward. In heterozygous instances, however, the phenotype of the organism is determined by which allele is dominant, meaning that one allele overrides the other.

In the case of eye color in humans, if someone inherits a blue allele and a brown allele, his or her eyes will be brown, because brown is a dominant genetic trait, requiring only one allele for expression. However, if that person had a child with someone who also carried a blue allele and both parents passed the blue trait down, the child would have blue eyes. This explains why blue-eyed children sometimes randomly pop up in a brown-eyed family: because someone in the family's genetic history had blue eyes.

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