. 2007 Aug 17;35(16):5593–5609. doi: 10.1093/nar/gkm598

Table 2.

Mathematical analysis of the segregation of tDNA sequences into Class I-II groups

	Class I					Class II

		Number of false-positive sequences^a		Probability (p) according to the statistical test^b			Number of false-positive sequences^a		Probability (P) according to the statistical test^b

	Number of sequences	SCP^c	ECP^d	SCP^c	ECP^d	Number of sequences	SCP^c	ECP^d	SCP^c	ECP^d
Saccharomyces cerevisiae	27	24	3	0.17	0.34	24	26	2	1.00	0.21
Schizosaccharomyces pombae	27	29	5	1.00	0.36	30	26	10	0.11	0.81
Caenorhabditis elegans	56	46	10	0.36	0.44	60	56	18	0.78	0.86
Drosophila melanogaster	44	31	4	0.11	0.81	34	44	8	1.00	0.89
Homo sapiens	60	57	34	0.89	0.13	58	43	12	0.07	0.55
Encephalitozoon cuniculi	22	22	2	0.86	0.20	23	22	8	0.61	0.91
Arabidopsis thaliana	75	63	1	0.60	0.03	71	54	1	0.38	0.03
Methanopyrus kandleri	18	8	2	0.15	0.22	15	8	3	0.04	0.18
Pyrococcus abyssi	25	20	2	0.58	0.26	20	16	2	0.39	0.20
Pyrobaculum aerophilum	23	21	3	0.91	0.19	22	15	6	0.44	0.53
Aeropyrum pernix	25	19	6	0.51	0.43	20	21	12	1.00	0.91
Archaeoglobus fulgidus	25	19	3	0.50	0.77	20	16	4	0.64	0.86
Halobacterium sp. NRC-1	25	16	2	0.04	0.31	20	25	3	1.00	0.26
Sulfolobus solfataricus	23	17	3	0.66	0.48	22	12	1	0.23	0.17
Sulfolobus tokodaii	23	20	3	0.89	0.31	22	16	3	0.46	0.28
Thermoplasma acidophilum	25	18	3	0.49	0.54	20	15	1	0.37	0.13
Ferroplasma acidarmanus	24	16	4	0.60	0.80	20	14	0	0.54	0.05
Methanosarcina barkeri	27	18	1	0.04	0.13	21	22	3	0.79	0.23
Methanococcus jannaschii	17	11	0	0.28	0.20	16	13	4	0.55	0.95
Methanobacterium thermoautotrophicum	20	13	2	0.44	0.66	16	14	3	0.77	0.68
Treponema pallidum	25	19	3	0.49	0.65	19	19	0	0.90	0.02
Borrelia burgdorferi	18	12	2	0.42	0.89	14	13	1	0.81	0.52
Chlamydia trachomatis	18	16	5	0.90	0.91	18	12	0	0.43	0.10
Synechocystis 6803	19	21	3	1.00	0.67	21	7	2	0.06	0.53
Anabaena	19	23	5	1.00	0.73	23	8	4	0.05	0.71
Lactococcus lactis	20	14	6	0.57	0.94	18	9	1	0.09	0.20
Listeria monocytogenes	19	13	1	0.41	0.29	20	15	6	0.72	0.96
Bacillus subtilis	23	16	4	0.55	0.63	21	17	2	0.76	0.24
Aquifex aeolicus	19	21	1	1.00	0.36	21	12	0	0.18	0.15
Mycobacterium tuberculosis	22	22	5	0.86	0.87	22	22	2	0.86	0.50
Deinococcus radiodurans	21	18	4	0.62	0.51	23	16	8	0.33	0.93
Neisseria meningitidis	22	20	7	0.74	0.97	20	14	6	0.37	0.89
Pseudomonas aeruginosa	20	21	5	1.00	0.61	21	13	5	0.27	0.67
Buchnera sp. APS	16	13	4	0.31	0.57	15	9	0	0.03	0.17
Bacillus halodurans	21	13	1	0.56	0.28	17	16	3	0.80	0.48
Thermotoga maritima	23	21	5	0.82	0.94	22	22	0	0.98	0.19
Campylobacter jejuni	19	12	4	0.28	0.89	15	12	1	0.34	0.20
Vibrio cholerae	25	22	2	0.58	0.42	22	17	3	0.35	0.46
Clostridium perfringens	20	18	3	0.55	0.65	18	20	1	1.00	0.17
Helicobacter pylori	19	13	2	0.56	0.66	16	11	1	0.32	0.32
Ralstonia solanacearum	20	23	6	1.00	0.91	23	13	2	0.17	0.46
Mycoplasma genitalium	18	17	6	0.89	0.98	17	14	1	0.62	0.23
Mycoplasma pneumoniae	19	17	5	0.89	0.94	17	14	1	0.61	0.23
Ureaplasma urealyticum	16	11	3	0.52	0.93	13	13	0	0.90	0.27
Xylella fastidiosa	22	22	5	0.98	0.64	22	15	2	0.46	0.17
Haemophilus influenzae	19	18	6	0.77	0.98	18	14	2	0.36	0.51
Escherichia coli	22	21	6	0.75	0.81	21	16	5	0.35	0.68
Rickettsia prowazekii	16	15	2	0.76	0.79	15	12	1	0.68	0.48
Yersinia pestis	21	22	7	1.00	0.86	22	15	4	0.32	0.61
Sinorhyzobium meliloti	43	22	22	1.00	0.60	22	12	24	0.00	0.39

^aSequences that based on an analysis could belong to both classes are named as false positives in the a priory class, to which they are not considered to belong to as explained in Figures 1 and 2.

^bThe bootstrap test quantifies the probability (P) of obtaining the observed number of false positives by pure chance, e.g. when the two classes are randomly defined from the same input tRNA pool (see Methods section). Cases with P ⩽ 0.25 are considered to be significant and are highlighted as bold.

^cThe strict consensus partition (SCP) analysis admits a sequence into a class if the sequence possesses all the elements that are strictly present in the given class.

^dThe extended consensus partition (ECP) analysis, on the other hand, admits a sequence into a class if the sequence does not possess any of the elements that are strictly absent from the given class. The species are arranged in blocks in the following order: Eukarya (top) Archaea (middle) and Bacteria (bottom) section.