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Table 2 Running time comparison on the challenging instances of the planted motif problem (DNA, |Σ| = 4, N = 20 sequences of length n = 600). Problem instances are denoted by (k,m, |Σ|), where k is the length of the motif implanted with m mismatches.

From: Efficient motif finding algorithms for large-alphabet inputs

Motif problem instances (k, m, |Σ|)
Algorithm (9,2,4) (11,3,4) (13,4,4) (15,5,4) (17,6,4) (19,7,4)
Stemming 0.95 8.8 31 187 1462 8397
MITRA [5] 0.89 17.9 203 1835 4012 n/a
PMSPrune [10] 0.99 10.4 103 858 7743 81010
RISOTTO [6] 1.64 24.6 291 2974 29792 n/a