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Table 2 More results on synthetic yeast-like data. Same as Table 1, except that the sequences have five embedded motifs (drawn from weight matrices that had 80% "polarisation"); this better mimics real data and also improves the performance of all programs.

From: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence

   q = 0.35 q = 0.45 q = 0.55 q = 0.65
5 embedded WM's
N s Prog N + N - Sen Er N + N - Sen Er N + N - Sen Er N + N - Sen Er
3 sigma+ 0 0 0.00 N/A 0 0 0.00 N/A 13266 0 0.44 0.00 29352 0 0.98 0.00
  sigma- 0 0 0.00 N/A 456 0 0.02 0.00 19028 0 0.63 0.00 29274 0 0.98 0.00
  dialign 78 0 0.03 0.00 60 0 0.02 0.00 2639 0 0.09 0.00 11383 40 0.38 0.00
  alignm 3067 506 0.10 0.14 11389 2153 0.38 0.16 24496 1217 0.82 0.05 28687 305 0.96 0.01
  clustalw 20814 9186 0.69 0.31 26730 3270 0.89 0.11 29341 659 0.98 0.02 29878 122 1.00 0.00
  mlagan 17160 12840 0.57 0.43 26930 3070 0.90 0.10 29716 284 0.99 0.01 30000 0 1.00 0.00
  tcoffee 10421 19579 0.35 0.65 20548 9452 0.68 0.32 28129 1871 0.94 0.06 29887 113 1.00 0.00
6 sigma+ 0 0 0.00 N/A 1625 0 0.03 0.00 36055 28 0.60 0.00 58596 0 0.98 0.00
  sigma- 452 42 0.01 0.09 5984 0 0.10 0.00 47264 26 0.79 0.00 58876 0 0.98 0.00
  dialign 510 144 0.01 0.22 1719 74 0.03 0.04 10250 0 0.17 0.00 33979 0 0.57 0.00
  alignm 3893 181 0.06 0.04 28300 1363 0.47 0.05 54487 1077 0.91 0.02 59496 170 0.99 0.00
  clustalw 42116 17884 0.70 0.30 53797 6203 0.90 0.10 58316 1684 0.97 0.03 59613 387 0.99 0.01
  mlagan 29458 30542 0.49 0.51 53833 6167 0.90 0.10 59427 573 0.99 0.01 60000 0 1.00 0.00
  tcoffee 25878 34122 0.43 0.57 47767 12233 0.80 0.20 58708 1292 0.98 0.02 59975 25 1.00 0.00
9 sigma+ 40 30 0.00 0.43 2300 0 0.03 0.00 56847 20 0.63 0.00 87436 0 0.97 0.00
  sigma- 322 30 0.00 0.09 5805 0 0.06 0.00 69821 120 0.78 0.00 88775 0 0.99 0.00
  dialign 450 80 0.01 0.15 2844 106 0.03 0.04 20179 0 0.22 0.00 59400 0 0.66 0.00
  alignm 10165 652 0.11 0.06 60374 2420 0.67 0.04 85011 933 0.94 0.01 89651 201 1.00 0.00
  clustalw 62461 27539 0.69 0.31 83233 6767 0.92 0.08 86738 3262 0.96 0.04 89167 833 0.99 0.01
  mlagan 33857 56143 0.38 0.62 81225 8775 0.90 0.10 88869 1131 0.99 0.01 90000 0 1.00 0.00
  tcoffee 43416 46584 0.48 0.52 76928 13072 0.85 0.15 89240 760 0.99 0.01 89990 10 1.00 0.00