The primer redundancy threshold value is the "global sequence identity" calculated as number of identical nucleotides in alignment divided by the full length of the shorter sequence. Based on the input threshold value, we construct clusters of sequences and search for identity.
A threshold of 0.81 (81%) for primer sequence redundancy was chosen for the analysis after plotting the threshold values from 80% to 100% against the redundant primer counts, based on the presence of the combined redundancy of the SSR primer sequences and repeat motifs. The following figure shows the redundant primer counts obtained for each of the individual threshold values.