Sex chromosomes are nonidentical but still homologous.
Alleles are slightly different forms of the same gene. They arise through mutation. Each diploid cell has a pair of alleles at each locus. Alleles on homologous chromosomes may be the same or different. Gene exchange between homologs is called crossing over and results in genetic recombination.
Independent assortment refers to the random alignment of each pair of homologous chromosomes at metaphase I of meiosis.