Representation of repetitive and non-repetitive sequences in genomic DNA. (A) Repetitive (gray) and non-repetitive (blue) segments are oriented vertically; the length of each subsequence is reflected by the height of the corresponding bar. (B) Repeat-masked region of human chromosome 10 showing alternating segments of repetitive and non-repetitive DNA. The high level of sequence fragmentation is clear, as is the wide range of sizes in both repetitive and non-repetitive segments. The horizontal line (red) indicates a segment length of 300 bp; a large number of non-repetitive sequences below this threshold are omitted when using naive tiling methods that simply avoid repeats. (C) Finer-resolution window of chromosome 10 before and after optimal sequence tiling. (Blue bars) Non-repetitive sequence that is covered in each case, (red bars) non-repetitive sequence that is lost. Non-repetitive sequences below the minimum size threshold are omitted when the sequence is tiled in a straightforward manner (left panel). Many of these are recovered after optimal tiling methods are applied (right panel). Note that a small number of repetitive nucleotides (short blue bars extending below the horizontal line) are included in the tile path to increase the overall sequence coverage.
