Dependence of negative discrimination on junction probe length. Intensity of probes of different length tiled across the junction between exon 9 and exon 12, which are not connected in the RB1 transcript. Light blue, length 30 nucleotides; red, 40; dark blue 50; green, 60. Vertical colored dotted lines mark where probes make a transition from completely within an exon to chimeric junction probes spanning both exons. At 35% formamide, the intensities of the 20-nucleotide probes are largely at background levels and are not shown, while 60-mers (green) show little decrease in signal while spanning a 'false' junction. Background level is shown by the black dashed line at the bottom of the figure.
Castle et al. Genome Biology 2003 4:R66 doi:10.1186/gb-2003-4-10-r66