Figure 2

Predicted repeat sequence secondary structures. These images represent the predicted secondary structures of transcribed forms of the repeat sequence families: a) BOX, b) RUP and c) SPRITE. The structures were generated from an alignment of 30 sequences from the S. pneumoniae ATCC 700669 genome in each case; only BOX elements with a canonical A₁B₁C₁ structure were used to produce the structure in a). The boundaries between the different subsequences are marked on the image. Base pairings are coloured according to their conservation in the alignment: the bolder the colour, the more strongly conserved the pairing of the bases, with different colours indicating different numbers of compatible interactions at equivalent sites in the structure (see key).