Table 7.

Sensitivity and Specificity of Multiple (2 and 3) Perfect Nucleotide K-mer Matches as a Search Criterion

	2,8	2,9	2,10	2,11	2,12	3,8	3,9	3,10	3,11	3,12
A. 81%	0.681	0.508	0.348	0.220	0.129	0.389	0.221	0.112	0.051	0.021
83%	0.790	0.638	0.475	0.326	0.208	0.529	0.339	0.193	0.099	0.045
85%	0.879	0.762	0.615	0.460	0.318	0.676	0.487	0.313	0.180	0.093
87%	0.942	0.866	0.752	0.611	0.461	0.809	0.649	0.470	0.305	0.177
89%	0.978	0.940	0.868	0.761	0.625	0.910	0.801	0.648	0.476	0.314
91%	0.994	0.980	0.947	0.884	0.787	0.969	0.914	0.815	0.673	0.505
93%	0.999	0.996	0.986	0.962	0.912	0.993	0.976	0.933	0.851	0.722
95%	1.000	1.000	0.998	0.993	0.979	0.999	0.997	0.987	0.961	0.902
97%	1.000	1.000	1.000	1.000	0.999	1.000	1.000	0.999	0.997	0.987
B. N,K	2,8	2,9	2,10	2,11	2,12	3,8	3,9	3,10	3,11	3,12
F	524	27	1.4	0.1	0.0	0.1	0.0	0.0	0.0	0.0

(A) Columns are for N sizes of 2 and 3 and K sizes of 8–12. Rows represent various percentage identities between the homologous sequences. The table entries show the fraction of homologies detected as calculated by equation 10. (B) N and K represent the number and size of the near-perfect matches, respectively. F shows how many perfect clustered matches expected to occur by chance according to equation 14 in a translated genome of 3 billion bases using a query of 167 amino acids.