However, when the proteins formed by the genes have their amino acids sequenced, there is no difference observed between the two. What is the most likely explanation for this observation?

The correct answer is: Variation in nucleotide sequences are located in those regions of the gene which do not affect the sequence of the protein due to genetic code degeneracy.

Explanation:

Proteins are encoded from the genes located in the chromosomes. The genes are made up of the heritable DNA (Deoxyribonucleic Acid) sequences. These genes are transcribed by the enzyme called RNA polymerase into mRNA (messenger Ribonucleic Acid) sequences in the nucleus. The mRNA is then translated into protein sequences by the Ribosome in the cytoplasm or the RER (Rough Endoplasmic Reticulum). The Ribosome reads the mRNA code in form of triplets, that is, three consecutive nucleotide are read as a single code that encode for a single amino acid. This triplet code that responsible for coding for a single amino acid is called a Codon. The Codons are degenerate in nature. This means that among the three nucleotide in a codon the first two nucleotide is specific for a particular amino acid. The third nucleotide is "wobble" in nature. This means that whatever may be the nucleotide in the third position it will not change the amino acid coded by the first two nucleotide. Hence, a single amino acid is coded by more than one codon. So, gene sequences showing variation in the wobble nucleotide position will encode for the same protein.