Repeat length refers to the maximal number of dinucleotide repeats within a primer. For example, the primer TCGCGCGCGT has a repeat length of 4, because it contains 4 consecutive GC-dinucleotides. Similarly to the run length, primers with too many repeats can lead to mispriming:
Primer | 5-TCGCGCGCGT-3' |
Template | 3'-AAAGCGCGCGCA -5' |
Primer | 5'-TCGCGCGCGT-3' |
Template | 3'-AAAGCGCGCGCA -5' |
The first, intended binding mode has a perfectly complementary primer, but the second, unintended binding mode also has a considerable number of complementary positions due to the large number of repeats.