Example breakpoint plot for two genomes (r_1) and (r_2) . Sequence segments encoding for the same gene are given the same color and annotated with the same gene name (g_1,g_2,g_3,g_4) , or (g_5) . The red intervals on the top and bottom of the figure show the predicted locations for a breakpoint. Black lines connect these locations to the identified related site in the other genome. For better readability, these lines are solid for the start and dashed for the end of a breakpoint. For example, the first red interval from positions eight to ten on the top left corresponds to breakpoint (g_1,g_2)_{1,2} . The connecting lines end at positions 8 and 30 in the bottom genome. Ideally, these lines should coincide with the corresponding boundary of the colored gene blocks for (g_1) and (g_2) . Here, this is only true for the (g_2) boundary. Thus, there is a distance of one of the predicted to the putative breakpoint location. There are no deviations for breakpoints (g_2,g_3)_{1,2},(g_4,g_5)_{1,2}, and (g_2,g_5)_{2,1} . Connecting lines that are not parallel to any of the colored areas indicate that the corresponding predicted locations cannot be allocated to any of the putative breakpoints. This is the case for the dashed line marked by an asterisk. The corresponding prediction is incorrect since there is no breakpoint between genes (g_3) and (g_4)
