Hi!
Two chromosomes that make up a homologous pair can differ. The reason why they would differ is because they contain different alleles for the same trait.
When these chromosomes are homologous, this just means that they have the same genes in the exact order. But, the actual sequences at some of the geni loci are a little different. They are different because they are alleles.
Hope I could help!
- Peaculiar
