Figure 1.

An example of a breakpoint. The synteny blocks (A_r, A_o) and (B_r, B_o) are consecutive on genome G_r but not on G_o. It defines a breakpoint on G_r between the two blocks. The sequence of the breakpoint is called sequence S_r. We define also sequence S_oA which flanks block (A_r, A_o) on G_o and is bordered by the next block (C_r, C_o) on G_o. The sequence S_oB is defined similarly, flanking block (B_r, B_o) on G_o and bordered by the next block (D_r, D_o) on G_o.