Table 1 Stage two algorithm

Ensure: reports if a matching key occurrence potentially belongs to an alignment

Require: query neighborhoods (left_query and right_query)

1: get database neighborhoods left_db and right_db

2: result_left ← 0; highest_left ← 0

3: result_right ← 0; highest_right ← 0

4: for i from 1 to L do

5:   result_left ← result_left + subst _score (left_db [i], left_query [i])

6:   if result_left > highest_left then highest_left ← result_left endif

7: end for

8: for i from 1 to L do

9:   result_right ← result_right + subst _score(right_db [i], right_query [i])

10:   if result_right > highest_right then highest_right ← result_right endif

11: end for

12: if highest_left + highest_right ≥ threshold $\mathcal{T}$then return true endif

13: return false