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Table 8 The number of the Subset 1 alignments at various levels of the in-frame identity. Fractions give the differences in the number of alignments by each method and Splign expressed as percentage of the total of sequences in the set.

From: Splign: algorithms for computing spliced alignments with identification of paralogs

  80% 85% 90% 95% 99% 99.5% 99.9% 100%
Splign 67342 67241 67105 66766 65767 64938 50968 35839
Sim4 63968 63723 63465 62986 61668 60622 47820 34033
  -4.68 -4.88 -5.05 -5.24 -5.68 -5.99 -4.37 -2.50
Spidey 65276 65182 65066 64766 63844 62867 48714 34451
  -2.86 -2.86 -2.83 -2.77 -2.67 -2.87 -3.13 -1.92
BLAT 64017 63932 63817 63545 62747 62115 49946 35632
  -4.61 -4.59 -4.56 -4.47 -4.19 -3.91 -1.42 -0.29
GMAP 66568 66463 66317 65956 64856 64058 50589 35680
  -1.07 -1.08 -1.09 -1.12 -1.26 -1.22 -0.53 -0.22
SPA 66777 66669 66516 66152 65042 64186 50669 35679
  -0.78 -0.79 -0.82 -0.85 -1.01 -1.04 -0.41 -0.22