ClustalW alignment of the 55 complete HORs of BAC BX248407. Alignment was obtained using the ClustalW program (35). The HORs are ordered from 1 to 55 as they appear in the published DNA sequence. DVN positions are indicated above the alignment from 1 to 141 and from 142 to 281. The remaining positions are not shown, as they are identical in all repeats; the same holds true for the other figures. DVNs shared by subset 1 (repeats 1-30) are shaded in red, those shared by subset 2 (repeats 36-55) are shaded in green, and those specific for subset 3 (repeats 31-35) are shaded in yellow. When DVNs are of two types at the same nucleotide position, purple shading is also used. Repeats 32 and 33 have presumably been generated by an unequal crossover event. Shared nucleotides are coloured in green for A, blue for C, red for T, black for G and "-" is used for deletions.