Figure 4

CODEHOP PCR primers derived from the IYG/GDTD sequence motif (A)(B) Sequence alignments across the IYG/GDTD motif as described in the legend to Figure 3. (C) The consensus amino acid sequence from the IYG/GDTD motif as determined by the CODEHOP software is presented (in bold and boxed) and the other amino acids found at each position are aligned vertically above the consensus amino acid. The coding strand sequence and the complementary strand corresponding to the "YGDTB" CODEHOP predicted by the CODEHOP algorithm are indicated with the sequences of the 5' consensus clamp in uppercase and the 3' degenerate core region in lowercase. The consensus sequence shows the extent of the sequence block determined by BlockMaker. The CODEHOP algorithm was unable to determine a 5' consensus clamp giving the required Tm due to the small size of the block. Therefore, three additional amino acid positions (in italics) were added to the C' terminal side of the block in (A) and (B) to allow visual inspection of the sequences to manually determine an additional 8 bp of the 5' consensus clamp which are underlined. The nucleotide sequences, relative positions and encoded amino acid sequences for the manually designed CODEHOPs, "IYG" and "GDTD1B" are also shown (see Table 1 for the exact nucleotide sequences of these anti-sense strand primers). The degeneracy of the primer pools is indicated in parentheses and the highlighted residues are discussed in the text. The CODEHOP primers, YGDTB, IYG and GDTD1B are all derived from the antisense DNA strand and are shown below the codons for the sense strand.