Putative amino acid sequence alignment.

The alignment starts at the 2nd amino acid position encoded by the exon 2 in MHCIIB. Sequences of chicken (Gaga_BLB1-haplB19 and Gaga_BLB2-haplB19, GenBank accession no. AB426151), barn owl (Tyal_DAB1-allele02, EU442602) and little spotted kiwi (Apow_DAB*allele08, HQ639687) [90] are shown for comparison. Dots represent identity to the sequence on top. Asterisks (*) indicate the amino acid positions under positive selection (based on CodeML analysis, model M8, posterior probability >0.95). Plus signs (+) mark the antigen-binding sites (ABS) in humans [64]. Tracts 1–7 depict codons contained in conversion tracts as given in Table 3. Black triangles represent the placement of two recombination breakpoints as detected by GARD.