Markup | Genome Research

Table 3.

Extremes of Tetranucleotide Usage Deviation in Coding and Noncoding DNA of Three Prokaryotic Genomes

		Zero Order Markov		Markov Chain
		Coding		Noncoding		Coding		Noncoding
Helicobacter pylori26695	(39.6%)[i]		(33.8%)
Overrepresented	AGCG	3.178	CCCC	4.804	CCGG	1.475	GAGT	1.408
	CGCT	3.066	GGGG	4.171	AGCG	1.456	ACGA	1.396
	AAAA	2.895	CGCT	2.969	GTAT	1.451	GCGT	1.379
	TTTT	2.830	AGCG	2.862	ACCG	1.443	ACGC	1.378
	GGGG	2.755	GCGC	2.667	CGCT	1.433	ATAC	1.355
Underrepresented	GTAC	0.018	GTAC	0.053	ACGT	0.088	ACGT	0.111
	ACGT	0.048	ACGT	0.055	GTAC	0.090	GTAC	0.204
	TCGA	0.049	TCGA	0.088	TCGA	0.111	TCGA	0.245
	AGTA	0.269	ACTG	0.316	GGCC	0.422	GGCC	0.403
	TACT	0.277	TACG	0.319	CGCG	0.427	CGCG	0.407
Campylobacter jejuni	(30.8%)		(25.5%)
Overrepresented	GCTT	2.793	GGGG	5.123	CAGG	1.655	GTCG	1.993
	AAGC	2.782	GGGC	3.656	CCTG	1.639	ACGC	1.578
	AGCT	2.343	GCGG	3.510	GTCC	1.483	GACG	1.533
	TTGC	2.275	GCCC	3.488	CGCC	1.473	CAAG	1.513
	GCAA	2.260	CCCG	3.443	GGAC	1.473	CCCG	1.496
Underrepresented	ACGT	0.085	ACGT	0.125	ACGT	0.283	ACGT	0.344
	CCGG	0.184	GTAC	0.294	CCGG	0.382	GATC	0.568
	GACG	0.288	CATG	0.308	GGCC	0.429	GGCC	0.622
	CGAC	0.288	CTGT	0.366	GCGC	0.457	CTGT	0.629
	GTAC	0.295	CGTT	0.386	GGTC	0.573	GCGC	0.634
Bacillus subtilis	(44.3%)		(38.6%)
Overrepresented	CAGC	2.290	TTTT	2.445	CGCC	1.247	GGAG	1.376
	GCTG	2.278	AAAA	2.371	GGTG	1.243	CTCC	1.372
	AAAA	2.265	CCCC	1.973	GGCG	1.235	CCGC	1.310
	TTTT	2.262	CTCC	1.957	CACC	1.227	GGTG	1.282
	CGGC	2.060	GGAG	1.937	CGAT	1.222	CGGC	1.282
Underrepresented	CTAG	0.170	CTAG	0.401	TAAG	0.708	GGCC	0.694
	ACTA	0.228	CTAC	0.422	CTTA	0.708	CTCG	0.729
	TAGT	0.234	TAGT	0.460	GGCC	0.743	CTCA	0.733
	TAGG	0.307	ACTA	0.467	ATCT	0.799	TGAG	0.743
	CCTA	0.314	GTAG	0.475	CGCG	0.802	CGCG	0.748

[i] G + C composition.