Suppl. figure 1 Four color sequence alignment. Satellite tartan DXZ1 (unordered). Samples of ten 2kb BamHI higher order repeats were subcloned from each of 5 X chromosome alpha satellite PACs and end-sequenced. Subclones from a PAC showing identical end-sequences were excluded because of potential doublet cloning. Identical end sequences of individual subclones A10BamHI-2 and A8BamHI-9 might indicate PAC overlap. In order to compact the sequence information of the 49 kb obtained, little squares were drawn for each nucleotide and painted using the ABI color code (see inset). Sequences are numbered beginning and ending with full BamHI recognition sequences and the gap size between end sequences was guessed. Each row approximates two 0.17 kb monomers. Position of centromere binding protein B-boxes (CENP-B) and primers X3-A and X4-A (Warburton and Willard 1992) used for array specific PCR from total genomic DNA (arrows) are indicated. Positions of a set of "common" variants abundant in more than one PAC sample are marked with asterisks, and restriction sites used to analyse variant fixation are shown. The display illustrates the high overall homogeneity of DXZ1 sequences within and throughout PAC samples, and gives an overview about the distribution of rare and common variants within higher order repeats.
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