A closer look at potential intra-chromosomal rearrangements. (A) For each stickleback chromosome, sea bass BAC clones can be determined whose BAC-ES pairs are inconsistently aligned in terms of distance or alignment orientation. If these pairs are incorporated in the mapping visualization as black lines, it can be found that edges of BAC-contigs are connected by these clones. It is very likely that these clones represent candidates that span intra-chromosomal rearrangements between stickleback and sea bass. (B) To increase significance of rearrangements and exclude rearrangements that were proposed due to chimeric BAC clones, the position of edges of BAC contigs was cross-checked on medaka chromosomes. For chromosome III we found that most of the rearrangements between sea bass and stickleback could be confirmed by comparison with medaka as a second reference genome. In total 214 potential rearrangements between sea bass and stickleback chromosomes could be pinpointed; about 65% of these were confirmed by comparison with medaka (see Table 2C, Table 3C and Table 4C). For visualizations of all chromosomes see supplemental data section. Rearrangements that were evaluated by PCR are labelled with the corresponding lanes in Fig. 4. For a detailed view of BACs ordered between 8.47 Mbp and 9.47 Mbp see Fig. 5.