Figure 1From: An efficient method to find potentially universal population genetic markers, applied to metazoansPrimer sequences. Sequences are written using the IUPAC code. We used the following codes to describe the rules that underpinned primer design: Capital letters represent the 5'clamp (non-degenerate), whereas small letters represent the degenerate part supposed to contain no mismatch whatever the species (based on known sequences, protein for CH primers or nucleotide for D or NH primers). CHX+Y-z: CodeHop primer with a 5'clamp (non-degenerate part) of X bases, and a 3' z-fold degenerate end of Y bases. CHX + Y-z + 2GT: CodeHop primer designed at the intron limit, which contains the first two bases of the intron (by mistake, we reversed the two bases in the single such case, i8F). DX-Y-mz-t: Classical degenerate primer of X bases long, Y-fold degenerate, containing z to t mismatches according to the species (despite degeneracy in primer design). NHX+Y-Z: We called this a 'Nucleotide-hop' primer, by homology with CodeHop primers, but design was based on nucleotide alignment; we designed a 5' clamp (non-degenerate) and degenerate the 3' end according to the set of nucleotide sequences available thus ignoring codons. NHX+Y-Z-mz-t: Same as above, but, despite primer degeneracy, there may remain mismatches in some species; in this case there are from z to t mismatches according to the species for which we have sequence data. For instance, a primer (D30-1-m0-2) actually does not contain ambiguity bases (-1: not degenerate), and contains 0 to 2 mismatches according to the species. Other symbols: * this primer was not used. # erroneous primer sequence, the subsequently corrected primer i13Rcor was not triedBack to article page