Table 3.

Number of detections per Mbp, average length, and average divergence for TRF, Mreps, Sputnik, STAR, and RepeatMasker, in the genome of four species.

		HS		DM	NC	SC
		All	Imperfect
detection number
	TRF {2,7,7;20}	2425	512	3119	2902	1822
	Mreps 1	1368	1084	1653	1371	879
	Sputnik {1,-6,7}	6589	361	7475	7665	5712
	STAR	395	260	311	343	182
	RepeatMasker	256	179	207	230	104
average length
	TRF {2,7,7;20}	16.07	28.84	14.24	14.61	13.85
	Mreps 1	22.96	24.99	20.04	20.93	20.28
	Sputnik {1,-6,7}	9.74	19.83	9.39	9.35	8.98
	STAR	39.89	49.80	31.07	32.86	33.12
	RepeatMasker	53.97	64.93	48.52	45.80	54.88
average divergence
	TRF {2,7,7;20}	1.60	7.59	1.61	1.47	1.35
	Mreps 1	12.39	15.65	11.46	10.10	11.71
	Sputnik {1,-6,7}	0.44	7.96	0.46	0.38	0.32
	STAR	7.45	11.33	7.98	6.44	7.59
	RepeatMasker	8.40	11.97	13.42	9.31	13.14

Both imperfect and all (perfect plus imperfect) detections are provided for the human genome while all detections only are reported for the other genomes. HS = Homo sapiens, SC = Saccharomyces cerevisiae, DM = Drosophila melanogaster, NC = Neurospora crassa. 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).