Homologous chromosomes are similar in all of these characteristics except:

Except alleles

Explanation:

Alleles are different versions of the same gene and that's because they have different DNA, even though it is slightly different it can make a lot of changes so that's why they have different alleles.

Allele is actually the variant form of some genes.

The best example for alleles we can find in the gene for blossom color in some species of flowers or plants. Only one single gene is controlling the color and we can see sometimes different versions of it. Those different versions are called Alleles.