Variation of amino acid residues in exon 2 of the MHC IIB genes. Included are 31 sequence variants from local populations of three-spined sticklebacks (Gasterosteus aculeatus). The variation for each residue is based on the number and frequency of substitutions and is calculated as y = 1 - Valdar01 score, as determined with the Scorecons server by Valdar . Dark bars and vertical arrows indicate residues involved in antigen binding, according to Brown et al. . Black arrows below the panel show positions of the primers used for amplification of the Exon 2: A (GAIIEx2startF) and D (GAIIExon2R_RSCA) are the new primers designed for this study; B and C1, C2 are the primers used in previous CE-SSCP assessments of the stickleback MHC [15, 19]. For visualisation, the variation plot was extended by 6 bases into the adjacent intron 2 (I, right side of panel). Despite the fact that an amino acid variation score cannot be calculated for an intron sequence, these 6 base pairs were fully conserved in all local sequences investigated so far.