Repeat Overview of Human Y Chromosome. This visualization of the first half of the Y chromosome is colored according to the best local alignment score. Chromosome Y was selected for the diversity of repeats. The second half of the Y chromosome has only a very small section near the end that has been sequenced so it is not included in this view. A) The bright red streak is the same 61-mer repeat seen in Figure 1B. B) The pure black streaks are regions of unsequenced N's. C) The green areas in the middle are 171-mer alpha satellite near the centromeres. D) A second region of alpha satellite repeat (with lower percent similarity) separated from the centromere starting around nucleotide #18,293,073 (March 2006 assembly). This is actually part of a large scale palindrome where the reverse compliment of the alpha satellite starts at # 18,822,065. E) The bright yellow region is a very large, 125-mer tandem repeat that comprises a quarter million nucleotides. F) Colors correspond to the frequency spectrum ranging from 1 - 250 nucleotide offsets. Brightness is based on the degree of local self-similarity, with brighter colors corresponding to better self-similarity.