The Hamming distance between two oligonucleotides, in our case, is number of not coinciding positions in these oligonucleotides.
AATGCGT
TAGGCTT
*A**G**T – Hamming distance is equal to 5.
If Hamming distance R between oligonucleotides from different sequences is lower than
the
threshold value ro, they are united into one class.
We recommend to use ro >( l/2 ).