Described are methods and systems for designing target-specific oligonucleotides of L-length. The method comprises a) parsing a polynucleotide target into overlapping sequences of N-length nucleotides, creating a kernel set; b) performing step a) reiteratively for each target until each it is associated with its own kernel set; c) removing N-length kernels from the kernel sets which are redundant; d) concatenating X-length nucleotide suffixes to each N-length nucleotide kernel to create L-length oligonucleotide sets; e) ordering L-length nucleotides within each set of step d) by their nucleotide position within the target; f) retaining or rejecting an L-length oligonucleotide, based on the presence or absence of each of the X consecutive and overlapping N-length kernels; and g) performing step f) reiteratively. Step g) can be modified to parse L-length oligonucleotide sequences into overlapping Y-length nucleotides to create a set of Y-length kernels; and h) removing certain kernels that meet specified conditions.