Fig. 2

Two examples of how the starting positions of Alu inserts were modified, taking into account the question of ‘microhomology’. Both examples (A and B) were taken from dbRIP, the Database of Retrotransposon Insertion Polymorphisms in Humans (http://falcon.roswellpark.org:9090/searchRIP.html). (a) Target site duplications (TSDs) are highlighted in bold and underlined; Alu sequence plus the poly(A) tail are italicised; the starting position of the Alu insert is indicated by an Arabic numeral. (b)Top sequence: ±10 bp flanking the top strand cleavage site (indicated by an arrow) deduced from a; lower sequence: whilst italicised sequence on the right side corresponds to the ten 5′-most nucleotides of the Alu insert illustrated in a, sequence not italicised on the left side was taken from the Alu insert’s respective consensus sequence at corresponding positions where applicable. Microhomology is shaded wherever applicable. Note that in A, re-assigning the first G of the originally annotated full-length Alu insert into the upstream TSD resulted in the generation of a one base-microhomology between the top strand’s 5′ overhang and the now 5′-truncated (1 bp) Alu insert. In B, re-assigning the 5′-most TGGCT of a 5′-truncated Alu insert into the upstream TSD resulted in the generation of more extensive microhomology