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Table 1 Number of detections per megabase, average length (bp), and average divergence (%) of detections for combinations of parameters in the human X chromosome.

From: Detecting microsatellites within genomes: significant variation among algorithms

   number length divergence
TRF     
minimum score     
  50 110 64.44 3.96
  40 202 47.65 3.68
  30 458 32.14 3.21
  20 2425 16.07 1.60
align. weights     
  2,7,7 110 64.44 3.96
  2,7,5 125 73.62 6.01
  2,5,5 136 76.44 7.13
  2,3,5 177 83.30 11.31
Mreps     
resolution     
  1 1368 22.96 12.39
  2 1539 28.11 18.47
  3 1636 32.21 22.15
  6 1712 39.80 26.51
Sputnik     
minimum score     
  20 154 34.55 1.13
  15 349 25.39 1.06
  8 4273 11.23 0.48
  7 6589 9.74 0.44
Sputnik     
mismatch penalty     
  -10 6555 9.33 0.01
  -6 6589 9.74 0.44
  -5 6818 10.12 1.19
  1. TRF alignment weights were set to {2,7,7} when varying the minimum threshold score, and the minimum threshold score to 50 when alignment weights varied. Mreps resolution was 1, 2, 3, and 6. Sputnik mismatch penalty was set to -6 when varying the minimum threshold score, and the minimum threshold score to 7 when varying the mismatch penalty. Match bonus and fail score were always fixed to 1 and -1, respectively. Divergence is deduced from the alignment of the detected sequence with the perfectly repeated corresponding sequence of focal consensus motif:
  2. divergence = (substitutions + insertions + deletions)/alignment length).