Detecting Key Structural Features within Highly Recombined Genes
Figure 5
Clustal W Alignments of nt Sequence Segments
Segments of sof sequences were extracted at the module start site, and included four extra nts upstream from the module start site in order to facilitate alignment. All extracted sequences assigned to a module were aligned using the Clustal W algorithm. The aligned sequences were trimmed to remove the extra 4 nt at the 5′ end, and the 3′ ends were trimmed to yield a total length of 24 nt, allowing for indels. Duplicates of the trimmed sequences were removed from the data shown. Aligned and trimmed sequences are displayed for four modules (A–D). Indicated in each panel are the number of iterations used to define each module and the number of unique trimmed sequence segments. Module 7 provides an example of a 3-bp insertion within the 24-mer backbone. Module 12 (D) provides an example of the module start site slippage that is observed in some high-iteration modules.