Figure 4.

Effect of window size on distinguishing paralogs and the amount of useable data. Panel A shows two homeologs and the sequence of paralogs from a homozygous fish. Paralogous sequence variants are in bold text. Two windows are represented (1 and 16), only the 16 nucleotide window can differentiate between the paralogs. Panel B shows a multiple sequence alignment of the expressed cDNA reads aligned to the gene sequence from Chrom 1a. Depending on the alignment criteria and the sequence similarity, the two different paralogs will both align to the sequence from Chrom 1a. The number of useable sequences depends heavily on the window size. The larger the window size, the less likely that a read will span the window length, but the more likely the paralogs will be distinguishable.