Distribution of intensities for all MPSS tags in Arabidopsis and rice. The 128,337 reliable MPSS tags in Arabidopsis were mapped to the probes on the tiling microarray. For each tag, we calculated the mean intensity, after converting the raw intensities into percentiles, from probes that lie within the start and end coordinates of an MPSS tag. Since MPSS tags are only 17 nt in length, we considered flanks of increasing nucleotide lengths, viz, 25, 50, 75 and 100. Along with the MPSS tag, these flanks translate to, on average, 2, 3, 5 and 6 probes, respectively. These regions correspond to, 67, 117, 167 and 217 bp in length, respectively, on the tile path. The plot in Figure 2A shows the percentage of MPSS tags for different bins of percentiles. A similar procedure was followed for calculating intensities for the 100,274 reliable MPSS tags in rice. The distribution of intensities for rice is shown in Figure 2B.