Fig. 4

Pairwise alignment of the top strand sequences (from 5′ to 3′) overlapping the presumed upstream breakpoints of the ABCD1 (Kutsche et al. 2002), APC (Su et al. 2000) and SERPINC1 (Beauchamp et al. 2000) genes and their respective Alu inserts. Dashes indicate gaps introduced in order to maximise alignment. Identical nucleotides are identified by vertical bars. The putative upstream breakpoints are denoted by vertical arrows. Alu sequences contained within the inserts are shaded. Unshaded Alu sequences are derived from the consensus Alu Yb9 sequence at corresponding positions. For the sake of simplicity, the sub-family of the precursor sequence that generated the shortest Alu insert associated with the 1444 bp deletion in the SERPINC1 gene (Beauchamp et al. 2000) was also arbitrarily designated Yb9 (this does not affect the conclusions drawn owing to the high sequence identity manifested by the members of the Alu sub-families; see Fig. 1)