Multiple species/isolate alignment of nucleotide sequence for exons 5 and 6, encoding codons 176-240 and intron 5. Primers for a multi-species pyrosequencing assay are indicated by arrows in the forward and reverse direction (200s and 200r) and for the pyrosequencing primer (200seq). The second round reverse PCR primer (200rs) used for L3 is shown. Coding region of exons 5 and 6 are shown in upper case with F200Y indicated in yellow and intron sequence is shown in lower case. Sequence degeneracy is indicated as shown for Figure 2. Consensus sequences were generated from the species indicated in Figure 2 with the absence of Cylicocyclus leptostomum (Cyc lep), Cylicostephanus minutus (Cyc min), Cylicocylcus ashworthi (Cyc ash) and the addition of the following three species; Coronocyclus coronatus (Cor cor), Cylicocyclus elongatus (Cyc elo), Cyathostomum pateratum (Cya pat). The 200 consensus (200 con) sequence is shown at the bottom of the alignment.