Figure 2
From: Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"
Diagrammatic structure of class A flexible patterns. Class A flexible patterns belong to the category of flexible patterns. Here "flexible" means that there is limited variation in the exact position of their conserved nucleotides. This is shown in the figure by the green arrows, indicating that the position of the conserved nucleotides may vary from one occurrence of the pattern to the next. The particular class of flexible patterns depicted here in the standard 5'-3' orientation is composed of two sets of conserved nucleotides. First, the patterns are shaped by a skeleton of regularly repeated Ts or TTs every 10 bp to 11.5 bp, spanning a maximum of 50 bp. These are called "skeleton nucleotides" and are symbolized by the black and dark grey Ts. The peripheral repeats of the skeleton, in dark grey, are sometimes absent from a given occurrence. The Ts of the central part, spanning 20 bp on average, are always present. Furthermore, class A flexible patterns are composed of a set of "inner nucleotides". These conserved nucleotides are represented here in dark blue. They can be any nucleotide but never Ts. They are located between the Ts of the skeleton and in the central part only.