Sliding window calculation of pp in genomic sequences surrounding IDA. The pp values were determined in 75-bp windows with 3-bp steps for A. thaliana chromosome sequences. The pp values in a region containing the small protein gene IDA and flanking sequences are shown. The diagram on top indicates the locations of exons (white box, untranslated regions; black box, CDS), introns (bent lines), transcriptional starts (small arrows), and intergenic sequences (thick gray lines). The six plots below the annotation diagram are the results of pp calculations in six reading frames (forward, +; reverse, −). The dotted line indicates pp = 0.2239, the threshold value for calling whether a 75-bp window is likely a CDS or not. The shaded areas highlight the overlap between IDA CDS and regions with a high pp. The arrow indicates the correct frame for the IDA CDS.
