Figure 3

The impact of defects is affected by the local sequence environment. Single base insertion profiles (hybridization signal plotted versus the insertion base position) of four 25 mer probe sequence motifs complementary to the same target URA. Following solution-background correction of the raw intensity data (Methods section) hybridization signals were normalized with respect to the largest hybridization signal in each of the four insertion profiles. The probe motifs 1 to 4 hybridize at different sections of the target oligonucleotide. Mean profiles (thick lines) were obtained from the moving average of the particular insertion profiles (particular hybridization signal are shown as faint symbols – profile 4 is shown in detail in Fig. 5A). The mean profiles 1 to 3 have a distinct minimum between base positions 15 to 20. The stabilizing CG-rich region following after base position 20 results in increased hybridization signals in profile 4.