Evolution of segmental duplications and principles for duplication-inferred mutations. A: (1) An intrachromosomal duplication event occurs during evolution, followed by (2) a mutation in one of the duplication copies, causing a G/A transition. (3) A historical mutation event is inferred from an alignment of the present-day duplication copy sequences. B: Sequences d1, d2, d3 and d4 are all segmental duplication copies of the same ancestral DNA sequence. (i) A single base mismatch observed in the alignment between duplication copies d1 and d2 lead to the inference of a G/A (A/G) point mutational event within this DNA sequence context. (ii) An identical mismatch in the same position as observed between d1 and d2 was observed between d1 and d3. Such instances were not recorded twice in the set of mutational events, as the mismatch most likely is a propagation of the result in (i). (iii) A C/T (T/C) base mismatch in the same position as observed between d1 and d2 was observed in the alignment of d1 (reverse strand) and d4. Since the complementary mutation has been recorded in (i), we did not record this mismatch as a mutational event, as it most likely was the result of propagation by duplication.