Algorithm 3.

Algorithm 3 Stem generation (independent of the alphabet size |Σ|)

Input: pair of k-mers a, b

Output: set of stems (patterns with wildcards) shared by a and b

if if d(a, b) ≤ mthen

Set stem = a

Set i = 0 … d positions in the mismatch region of the stem as in b

Place j1 = 0 … d − i wildcards inside the mismatch region

Place j2 = 0 … m − max(d − i, j1 + i) wildcards outside the mismatch region

end if

ifd(a, b) >mthen

Set stem = a

Fix i = d − m … m positions in the mismatch region of the current stem as in b

Place j = 0 … m − i wild-cards in the remaining d − i positions in the mismatch region

end if

Output resulting stems (patterns with wildcards)