Evaluation of seven potential rearrangements between stickleback chr III and the corresponding sea bass linkage group 10 by means of PCR. Primers were designed on sea bass BAC-ES representing the ends of BAC contigs that seem to be connected by a rearrangement spanning BAC-clone. PCR was performed on the connecting BAC to proof the overlap with both BAC contigs and on genomic DNA to check that the PCR product was a unique marker in the sea bass genome. The amplified markers are shown above, for each rearrangement the first and second lane represents the markers amplified on the rearrangement spanning BAC, the third and fourth lane shows the same markers amplified on genomic sea bass DNA. Lane 1-4: bassbac140-o20/stickleback chr III 6.6 Mbp <> 2.66 Mbp. Lane 5-8: bassbac-137j6/stickleback chr III 14.06 Mbp <> 16.65 Mbp. Lane 9-12: bassbac-1g24/stickleback chr III 16.14 Mbp <> 10.6 Mbp. Lane 13-16: bassbac-38h23/stickleback chr III 0.5 Mbp <> 10.55 Mbp. Lane 17-20: bassbac-52b18/stickleback chr III 15.89 Mbp <> 10.64 Mbp. Lane 21-24: bassbac42b12/stickleback chr III 0.457 Mbp <> 10.44 Mbp. Lane 25-28: bassbac49h3/stickleback chr III 0.035 Mbp <> 0.311 Mbp. Each of the seven BACs had overlaps with the two BAC-contigs predicted by the comparative mapping approach. 12 out of 14 markers were unique in the sea bass genome. 2 markers (Lane 20 and 28) could not be amplified using genomic DNA as a template.