Figure 3

Graphical adaptation of BLAST alignments of palindromic segmental duplication (PSD) regions from chromosomes 8p23, 4p16, 11q13 and 3q21 showing high sequence similarity between inverted members of PSD pairs with relatively equal internal spacing between the loci. Horizontal bars containing graphical alignment represent identical sequences from each 'fugued' chromosomal region, as indicated. All sequence identities with an E-value of e^-20 and ≥ 90 per cent identity are displayed graphically between the horizontal bars, colourised based on alignment length, as described in Figure 1. The bar directly above the alignment represents either PSDs or SDs in tandem orientation (TSDs). (a) T wo overlapping PSDs are present on chromosome 3q21, one showing a similar but unique structure to 8-4-3-11 family-related PSDs and one internally flanking chromosome 3-specific PSD; no common inversion polymorphism is reported for this region. (b) PSD mediating the inversion on chromosome 4p16 with less complex structural features. (c) PSD mediating the common inversion on 8p23 harbouring multiple internal TSDs, especially on the left arm. (d) PSD at chromosome 11q13, with sequence structure and internal spacing similar to PSD regions at 8p23 and 4p16 but without known common inversion polymorphism.