Figure 5

(A) Single base insertion defect profile (hybridization signal plotted against the insertion base position; following solution background-correction of the raw intensity data, hybridization signals were normalized with respect to the largest hybridization signal in the insertion profile) of the probe sequence motif 3'-CACGTCGTCTCCCCTCACCTTAAG-5' (complementary to the target URA). Symbols correspond to insertion bases (A red crosses; C green circles; G blue stars; T cyan triangles). The mean profile (black line), obtained from the moving average (including all 4 insertion types) over positions p - 2 to p + 2 shows the common positional dependence. Insertions to the left and to the right of an identical base (Group II bulges – see text) result in identical probe sequences. (B) and (C) Deviation profiles. Positional influence is mostly eliminated by subtraction of the mean profile. Elevated intensities are observed for Group II bulges (e.g. C insertions at positions 11 to 15, 6 to 7 and 18 to 20 or G insertions at positions 4 to 5 and 7 to 8). A very distinct increase of the hybridization signal is observed for C insertions into the subsequence TCCCCT in the middle of the sequence. As shown in (C) Group II bulges (red markers) have significantly higher intensities compared to Group I bulges (blue markers).