Figure 6

Locations and efficiencies of putative origins on the three chromosomes. The chromosomes are shown as consecutive horizontal lines, 1 Mbp per line. The position of the centromere on each chromosome is indicated by a light yellow rectangle. The positions of origins classified as strong, medium, weak or very weak are identified by vertical lines. The lines range in color from red (strong) to brown (very weak) and from long (strong) to short (very weak). The positions of potential origins below the detection limit are indicated by the text character, "0", and ambiguous origins (where our probes were too widely spaced to permit confident evaluation) are shown by the character, "?". Small circles above each chromosome line indicate the positions of origins identified by Heichinger et al. ([14]; top row of circles; light blue), AT islands (next row of circles; magenta), origins identified by Feng et al. [34] in cds1 Δ cells (next row; orange) or in wild-type cells (next row; purple), and pre-RCs identified by Hayashi et al. ([15]; bottom row; dark blue or red circles or squares). For the pre-RCs, the colors blue and red distinguish the pre-RCs that are late/weak or early/strong, respectively. The circles represent pre-RCs that are not affected by deletion of cds1, while the squares indicate pre-RCs that replicate to a greater extent in cds1 Δ cells than in wild-type cells [15]. The positions of origins where the signals (our measurements; Additional Files 4, 5, 6) for both checkpoint-mutant strains were significantly greater than the signal for wild-type cells are indicated by the text character, "C", and the positions of origins with the opposite characteristic (wild-type signal significantly greater than the signals from both checkpoint-mutant strains) are shown by the text character, "W". A pale green background indicates a large region with a high frequency of stronger origins. A pale yellow background indicates a large region with a high frequency of weaker origins. (A) chromosome 1; (B) chromosome 2; (C) chromosome 3.