Fig. 6.

—Distribution of sequences into comet-like clusters near abundant sequence variants. (A) PCA projection on principal components 1 and 2 of the normalized 5-mer frequency vectors for all sequences from the XmnI monomer data set is shown here with a lower point density than the one shown in figure 1. Sequences corresponding to highly repeated sequences 1 (yellow), 5 (red), 11 (green), and 30 (blue) are highlighted. (B), (C), and (D) Only the region of the PCA projection corresponding to the dotted rectangle (i.e., to the C1 family) is shown. (B) Sequences from the data set that correspond to single nucleotide variations from sequences 1, 5, 11, and 30 are shown using the same color code as in (A). (C) Sequences from the data set that correspond to single nucleotide difference from sequences 3, 7, and 19 are shown in red, green, and blue, respectively. (D) Sequences from the data set that correspond to single nucleotide difference from sequences 2, 8, 12, and 15 are shown in red, green, blue and yellow, respectively.