Nucleotide sequences may be displayed in codons, in this case the numbering follows that for protein sequences. The codon 5' to this is numbered -1. All numbering is based on the reference sequence. The single letter amino acid code is used in all protein alignments. Nucleotide sequences may be displayed in codons, in this case the numbering follows that for protein sequences.
Some tools provide sequence alignments where identity and mismatches are highlighted.
In these tools, the following conventions are used. The entry for each allele is displayed in respect to the reference sequences. Non-identity to the reference sequence is shown by displaying the appropriate base at that position. In protein alignments, sequence following the termination codon, will not be marked and will appear blank. These conventions are used for both nucleotide and protein alignments.