Figure 5

CODEHOP PCR primers derived from the "DFAS/QAHN" sequence motif (A)(B) Sequence alignments across the "DFAS" motif as described in the legend to Figure 3. The non-conserved amino acids in the IHV sequence are highlighted (C) The consensus amino acid sequence from the "DFAS" motif as determined by the CODEHOP algorithm is presented (in bold and boxed) and the other amino acids found at each position are aligned vertically above the consensus amino acid. The sense-strand "HNLCA" CODEHOP predicted by the CODEHOP software is indicated with the 5' consensus clamp in uppercase and the 3' degenerate core region in lowercase. The sequence, relative position and encoded sequences of the manually designed CODEHOPs, "DFA", "DFASA", "QAHNA" and "SLYP1A" are also shown (see Table 1). The degeneracy of the primer pools is indicated in parentheses. The codons found in the different herpesvirus sequences encoding the serine (S), block position 6, in the "DFAS" motif were all of the "AGY" type serine codons, so the manually derived primers utilized those codons exclusively at that position.