Fig. 3

The distribution of parallelisms across four pairwise alignments. Aligned sequences are depicted as horizontal black lines. Protein coding features are represented by thick red boxes, with untranslated sequences marked by the thinner rectangles. The positions of parallelisms within each alignment are shown by vertical gray lines connecting the two aligned sequences. a Alignment between duplicons spanning HLA-DRB1 and HLA-DRB5 on 6p21. b Alignment of segmental duplications that include olfactory gene clusters in the subtelomere of the short arm of chromosome 1. Several clusters of parallelisms between these duplicons are evident, including six parallelisms between OR2T3 and OR2T34 and a group of four in the ~5 kb region downstream of OR2T29 and OR2T5. c Alignment between the tandem inverted RCHE/RHD duplication on 1p36. d Alignment involving a duplicon spanning the 3’ end of CYP2F1. A cluster of parallelisms in the middle of this alignment includes sites in the 3’ UTR of this gene