Position and nucleotide context around UGA codons.

A. The amino acid position of the last or most 3’ UGA codon in the query sequence alignment was divided by the total length of the top hit in the BLASTx comparison and plotted as a histogram to indicate where the UGA codons were found relative to the total length of the subject sequence. Comparisons to P. marinus (red) and the reference sequence (black) databases are shown for AT biased sequences with increased BLASTx scores when using alternative genetic codes. B. The composition before and after UGA apparently encoding stop versus UGA as tryptophan, based on increased BLASTx scores when UGA was translated as tryptophan. In frame UGA as stop for 457 non-redundant sequences from the parasite fraction were compared to 333 in UGA as tryptophan using two sample logo with the t-test. The size of the nucleotide shows the relative enrichment or depletion of each nucleotide in the upstream and downstream positions, but is shown only for nucleotides enriched or depleted at a p-value below 0.05 (see S2 Fig for raw frequency values).