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Table 14 Filtering of genomic repeats by different methods. Q1 is the fraction of masked words. Q2 is the fraction of words masked exclusively by the method. In case of RM and WM, a word was considered masked if all its bases were masked. The timing in each test was obtained using a single instance running on Intel Xeon 2.33 GHz/8 GB Linux box.

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

   RepeatMasker WindowMasker Compart
Human Q1(%) 46.79 28.81 17.68
  Q2(%) 31.03 12.23 5.41
  time (min) 6077 131 7
Mouse Q1(%) 40.55 28.61 17.71
  Q2(%) 25.24 12.41 5.46
  time (min) 5955 117 6