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Table 2.

Comparison of Tetranucleotide Usage Deviation in Species-Specific Bacteriophages, Plasmids, and Horizontally Acquired Genetic Elements and Their Host Strains and Controls.

Plasmid, Bacteriophage, or Island (bp)	Comparison Genome or Plasmid	R^2a Zero-Order Markov	R^2aMarkov Chain
Deinococcus radiodurans megaplasmid	Chromosome 1	0.893	0.811
(177,466)	Chromosome 2	0.915	0.805
	Bacillus subtilis	0.721	0.053
D. radioduransplasmid	Chromosome 1	0.573	0.348
(45,704)	Chromosome 2	0.588	0.372
	Megaplasmid	0.708	0.420
	B. subtilis	0.312	0.110
Escherichia coli O157:H7 plasmid pO157	E. coliO157:H7	0.634	0.645
(92,084)	E. coliK12	0.574	0.590
	Salmonella typhi	0.533	0.615
	Haemophilus influenzae	0.185	0.121
Yersinia pestis plasmid pCD1	Y. pestis	0.800	0.684
(70,559)	E. coli K12	0.669	0.503
	H. influenzae	0.448	0.252
Enterobacterial-specific phage HKO22	E. coliK12	0.805	0.592
(40,751)	S. typhimurium	0.717	0.606
	Mycobacterium tuberculosis	0.269	0.108
Enterobacterial-specific phage P22	E. coliK12	0.697	0.547
(41,724)	S. typhimurium	0.608	0.551
	M. tuberculosis	0.195	0.127
Pseudomonas-specific phage D3	Pseudomonas aeruginosa	0.757	0.410
(56,425)	E. coliK12	0.351	0.305
Pseudomonas-specific phage ΦCTX	P. aeruginosa	0.767	0.681
(35,559)	E. coliK12	0.356	0.141
Methanobacterium-specific phage ΘM2	Methanobacterium thermoautotrophicum	0.709	0.210
(26,111)	Methanococcus janaschii	0.344	0.090
	Pyrococcus abyssi	0.275	0.122
Mycobacterium-specific phage D29	M. tuberculosis	0.450	0.266
(49,136)	Mycobacterium leprae	0.290	0.184
Mycobacterium-specific phage I5	M. tuberculosis	0.428	0.342
(52,297)	M. leprae	0.270	0.218
Helicobacter pylori J99cag Island	H. pylori	0.726	0.618
(36,608)	C. jejuni	0.632	0.144
	B. subtilis	0.214	0.087
Vibrio cholerae integron island	Vibrio cholerae chromosome 1	0.394	0.047
(125,300)	V. cholerae chromosome 2	0.499	0.205
	E. coliK12	0.220	0.005
	B. subtilis	0.208	0.010
Campylobacter jejuniextracellular	C. jejuni	0.470	0.194
polysaccaride biosynthesis cluster	H. pylori	0.299	0.029
(28,313)	B. subtilis	0.114	0.048

[i] Determined by linear regression comparisons ofF(W) for all tetranucleotides.