PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches

Table 2 Number of operations used for Algorithm 1: number of mismatches (\(n_m\)), length of a periodic block (T), total number of seeds to be validated (# tests), averaged numbers of SIMD OR (\(n_{\text{OR}}\)), XOR (\(n_{\text{XOR}})\) and standard addition (\(n_{add}\)) operations for each binary block as an absolute number or as percentage of \(n_{\text{OR}}\) operations

\(n_m\)	T	# tests	\(n_{\text{OR}}\)	\(n_{\text{XOR}}\)	% of \(n_{\text{OR}}\)	\(n_{add}\)	% of \(n_{\text{OR}}\)
2	30	2391	218	194	89	74	34
2	35	6259	174	150	86	51	29
2	40	66,542	206	182	88	67	33
2	50	330,586	161	137	85	45	28
2	60	7,780,954	169	145	86	49	29
3	25	6296	459	419	91	188	41
3	29	88,578	955	906	95	464	49
3	33	595,263	387	350	90	145	37
3	38	14,780,813	571	532	93	241	42
4	25	4989	2858	2724	95	1630	57
4	29	68,931	3405	3274	96	1893	56
4	33	966,747	4292	4153	97	2361	55
4	38	32,240,220	1501	1437	96	730	49
5	25	780	105,377	97,501	93	77,081	73
5	29	13,668	30,507	28,945	95	19,946	65
5	33	229,001	14,869	14,342	96	8865	60
5	38	9,574,775	6432	6238	97	3566	55
6	25	283	80,726	74,048	92	61,606	76
6	30	7520	32,220	30,638	95	21,071	65
6	35	200,437	29,377	28,254	96	18,128	62
6	38	502,937	320,811	305,715	95	208,510	65
7	25	83	176,631	158,692	90	146,921	83
7	30	6205	7026	6672	95	4362	62
7	33	5173	717,404	665,819	93	526,252	73
7	38	448,976	31,566	30,395	96	19,488	62
8	30	728	92,676	85,827	93	70,045	76
8	35	1909	32,199,261	29,015,989	90	26,230,401	81
9	30	177	2,632,939	2,267,998	86	2,547,863	97
9	35	1784	1,722,183	1,556,851	90	1,419,823	82

ISSN: 1471-2105