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Table 4 Correct alignments using gapmis, gapmis_one_to_one_f, gapmis_one_to_one_onf, and needle.

From: libgapmis: extending short-read alignments

Species Length of queries [bp] Gap occurrence frequency gapmis gm -f 2 gm -f 3 gm -onf 2 gm -onf 3 needle
AT 100 2.4 × 10-5 999,099 998,404 997,561 999,207 999,259 999,126
AT 150 2.4 × 10-5 998,805 998,171 997,542 999,024 999,152 999,115
BV 100 1.7 × 10-5 999,361 998,868 998,229 999,432 999,459 999,353
BV 150 1.7 × 10-5 999,196 998,771 998,249 999,347 999,432 999,378
HS 100 5.7 × 10-6 999,809 999,615 999,419 999,822 999,825 999,782
HS 150 5.7 × 10-6 999,795 999,606 999,408 999,817 999,825 999,793
  1. The correct alignments of 1, 000, 000 pairs of simulated sequences with various observed gap occurrence frequencies using gapmis, gapmis_one_to_one_f, gapmis_one_to_one_onf, and needle. Each of the datasets consists of 1,000,000 pairs of sequences; the highest number of correct alignments for each dataset is shown in bold.