Structure of the 2R b / +bbreakpoint junctions. At top and bottom is a schematic overview of the 2Rb/+band 2Rc/+carrangements as represented by the PEST and M reference sequences, respectively. Horizontal black bar represents a segment of chromosome 2R. The relative position and orientation of chromosomal arrangements is indicated by labeled brackets, and centromeric/telomeric ends of 2R are indicated as Cen and Tel, respectively. Shaded arrows indicate the orientation of the arrangements, and labels inside the arrows (e.g., 11C) provide the cytogenetic subdivision in which the breakpoint junction occurs. Blue and gray boxes labeled with the corresponding cytogenetic subdivision represent flanking sequence outside of chromosomal rearrangements; red boxes represent repetitive DNA. The central part of the diagram provides a more detailed structural analysis of the color-coded breakpoint regions. Throughout, color is used to indicate homologous sequences between alternative arrangements, except for rectangles filled by patterns, which represent exclusive insertion events. Horizontal blunt arrows shaded in olive green and orange are sequences present once in the 2R+barrangement that have been duplicated into a palindrome in the alternative 2Rb arrangement. The red vertical arrows represent the putative breakpoints, positions where unique sequence ends and repetitive sequence framing both ends of the arrangement (red blunt arrows) begins. Black arrows at the ends of each diagram represent continuing chromosomal sequence; dotted lines represent gaps in the assembly. Blue curved lines represent sequence linked by mate-pair information. Asterisk framed by a white box indicates the chromosomal region targeted by the PCR diagnostic assay; see text and Figure 4 for details. Not to-scale.