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Table 4 Representative search times for K = 6

From: MICA: desktop software for comprehensive searching of DNA databases

Query Chromosome 1 Human Genome
  Time (sec) Hits Time (sec) Hits
Nondegenerate 3-mers 1.1 [0.80] 6.96 × 106 14.8 8.90 × 107
Nondegenerate 4-mers 0.28 [0.16] 1.69 × 106 4.2 2.17 × 107
Nondegenerate 6-mers 0.043 [0.0032] 160,702 0.96 2.05 × 106
Nondegenerate 8-mers 0.079 [0.011] 16,631 1.6 213,099
Nondegenerate 15-mers 0.088 [0.0074] 1.39 1.8 5.81
Nondegenerate 30-mers 0.13 [0.0076] 1.03 1.8 1.24
Nondegenerate 100-mers 0.12 [0.0050] 1.01 1.7 1.02
Nondegenerate 1000-mers 0.094 [0.0023] 1.00 1.3 1.00
Alu 30-mer fragment 0.12 [0.0055] 1,130 2.5 14,041
GDGCHC (Bsp 1286I) 0.13 [0.031] 398,999 2.5 4,776,086
GCCNNNNNGGC (Bgl I) 0.44 [0.15] 44,761 6.2 520,776
ACNNNNGTAYC (Bae I) 1.40 [0.37] 20,243 21.1 259,837
  1. Both DNA strands were searched using K = 6. The queries and the procedure were as described in Table 3, except that each 3- or 4-mer was extended to a partially degenerate 6-mer.