Table 1.

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

		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

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:

divergence = (substitutions + insertions + deletions)/alignment length).