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. 2003 Jul 1;31(13):3763–3766. doi: 10.1093/nar/gkg524

Figure 4.

Figure 4

CODEHOP designer output. The biased Block D of the DNA methyltransferases (Fig. 1) was used to design CODEHOP PCR primers using the default 60°C (A) or 65°C (B) annealing temperature parameter. The consensus amino acid residues and predicted CODEHOP PCR primers (5′–3′) are shown. The preferred CODEHOP has 16-fold degeneracy. The change in the 5′ clamp length obtained with the higher annealing temperature setting in (B) is evident. The anti-sense CODEHOP PCR primer designed from the complementary strand of the DNA encoding Block F of the DNA methyltransferase sequences is shown (C). The primers shown here are very similar but not identical to those utilized in our previous study to identify new DNA methyltransferases (1), since the codon usage table for A.thaliana has changed since 1998. The degeneracy and length for each core and the length and annealing temperature of each clamp are indicated.