Detection and analysis of evolutionarily conserved sequences on human chromosome 21 by cross-species comparisons using high-density arrays. (A) The chromosome 21 arrays were designed using nonrepetitive sequences and hybridized with syntenic mouse and dog BACs(horizontal lines). A low-magnification view of a fluorescence hybridization image of an array is shown. (B) Chromosome 21 reference sequence was tiled as 25-mer oligonucleotides (probes). Each nucleotide of the reference sequence was interrogated by four probes: one probe complementary to the sequence and three probes noncomplementary at the central position. When the fluorescent intensities (white squares) of the complementary probes are greater than that of the noncomplementary probes, similarities between the tiled human 21q sequences and the hybridized animal DNA exist. (C) (Top) Enlarged view of a 21q array hybridized with syntenic dog BAC DNA. Two 30-nt intervals, one with high conformance between human and dog sequences (97% conformance, red rectangle) and one with low conformance between human and dog sequences (60% conformance, blue rectangle), are shown. (Bottom) For the conserved sequence with high conformance, the 29 conforming nucleotides are indicated in red. For the conserved sequence with low conformance, the 18 conforming nucleotides are indicated in blue. (D)CONSEQ plots showing the conserved sequences (red peaks that are highlighted yellow) detected on the above 21q array relative to their position in the human reference sequence (horizontal axis) and their percent conformances (vertical axis). The high-conformance (97%) conserved sequence has been merged with neighboring conserved sequences to form a 190-nt element. The low-conformance (60%) conserved sequence is an isolated 30-nt element. (Small tan rectangles) Positions of interspersed repeats, which compose ~33.5% of chromosome 21 sequence and were not tiled on the arrays (Supplemental Table 4, http://www.genome.org); therefore, conformance information is absent.

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