Figure 2

Visual investigation of CRISPRs in the Sulfolobus solfataricus P2 genome (RefSeq entry NC_002754). From A to D, please note that the x-axis scale varies, depending on the degree of magnification. A. Linear pygram of the complete genome sequence. The normal (N) strand view is above the black horizontal line, and the reverse complement (RC) strand view is below this line. The x-axis corresponds to the sequence coordinate system. The y-axis corresponds to eMR size, and horizontal grey lines representing eMRs containing 100 and 1000 nucleotides are displayed on both N and RC views. The small blue boxes located between the black line and the N and RC views indicate eMR frequency. B. Logarithmic Pygram of the same genome. The small red boxes located between the black line and the two-strand views highlight the most frequent repeat in the genome. C. Pygram with two zoom lenses. The first yellow box represents a lens that magnifies the x-axis of the sequence region 300 times, between coordinates 1,233,000 and 1,240,500. The second lens magnifies the x-axis of the sequence region 500 times, between coordinates 1,257,000 and 1,261,500. Since the y-axis scale is linear, the y-axis was magnified 20 times in the lens regions for a better view of small repeat organization (note the shift of the y-axis grey lines; inside the lens, the two remaining grey lines are for repeats containing 10 and 100 nucleotides). The small red boxes located between the black line and the two-strand views highlight the most frequent repeat in the genome. D. Details of two CRISPRs. The pygram displays the first 1500 nucleotides of the first CRISPR presented in Figure C, followed by the last 700 nucleotides of the second CRISPR from Figure C; for the sake of clarity, the black vertical arrow has been added to mark the 26.5 kb gap separating the two CRISPRs. The grey horizontal line inside the lens marks repeats containing 10 nucleotides, whereas the grey lines outside the lens designate repeats containing 10 and 100 nucleotides. In the centre of the pygram, the red rectangle highlights the most repetitive eMR identified in the genome. The main constituents of CRISPR are annotated just above the x-axis numbers: the leader sequence and CRISPR units are underlined with blue and grey rectangles, respectively.