Figure 7.
Sensitivity difference profiles obtained by fitting the positional dependent NNN model to the logged intensity difference of each probe pair, Δ = log IPM - log IMM. The profiles are sorted according to the central base in the NNN-terms of the PM probes, xBy with B,x,y = A,C,G,T. Only profiles of triple degenerated homo-motifs and the respective 'mirror' motifs with complementary center base are highlighted by colored thick lines. The upper panel gives the respective base pairings in the duplexes of the PM and MM (upper and lower case letters refer to the probe and the target respectively). The dotted rectangles refer to the middle tripe (sequence position k = 11 ... 13). The triple terms within this range are different for PM- and MM-probes. Their amplitudes refer to the respective swap of the middle base at k = 13 in the sequence of the MM-probes. Note the symmetries of the obtained profiles for complementary degenerated triples. The PM and MM probe sequences are identical outside the middle range. The absence of large amplitudes indicates that the intensities of both, PM and MM probes, similarly respond to sequence effects.