Figure 5

Visualization of k -mer frequencies in a 453 kbp assembly of four BAC sequences derived from maize chromosome 8. A 100 kbp segment (range 70,001–170,000 nt) is shown. In the first two tracks transposable elements are shown in red while genes are shown in blue (exon/intron structure not shown). The third track, global k-mer frequency (GKF), shows for each position of the mentioned region (X-axis) the average frequencies λ(k, v, S) (Y-axis) of the k-mer v beginning at this position. Here S is the 0.45 × WGS set mentioned above. The fourth track, local k-mer frequency (LKF), shows λ(k, v, R), where R is the larger 453 kbp region under scrutiny. RepeatMasker results using the MIPS REcat repeat libraries are given alongside sequence masked using absolute frequency thresholds of 1, 2, and 3. Three genes (boxed) related to a selenium binding protein apparently arose by tandem duplication and have high LKF compared to other non-TE genes in the assembly.