Figure 2.

(A) Alignment of finished sequence from the two haplotypes, superimposed on the annotation of repetitive DNA (gray bars). In many cases the haplotype-specific sequence and its boundaries coincide with repetitive sequence, indicating that a repetitive DNA element (often a SINE) has inserted in one of the two haplotypes. Black lines indicate all BLASTN alignments between finished sequence from the two haplotypes. (B) Illustration of the repetitive sequences and alignments flanking a 6-kb interval specific to haplotype A. This is consistent with a deletion in haplotype B mediated by recombination through SINE elements.