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An example of duplication inference. (a) The original match regions in a sequence S. S contains 10 matches 
for regions Ai and 
where 1 ≤ i ≤ 10, and the box shows the location of an intraposed duplication which is discussed in Sections 2.4 and 2.5. (b) The self-alignment of the original sequence. (c) The self-alignment after rolling back a duplication. (d) The self-alignment after rolling back another duplication. See Section 2.3 for details.
