77.4%GC3 content

41.7Effective codons (Nc)

1,229Coding sequences

2/26GC3 rank here

Genetic code

NCBI table 11 (Bacterial, Archaeal and Plant Plastid), covering chromosomal coding sequences. Sense-codon assignments match the standard code; initiation differs. Which code applies where.

What distinguishes this table

The most constrained choice in M. bovis (bovine/elephant TB) is isoleucine: of its 3 synonymous codons, ATC takes 80% of the family. Glutamate sits at the other end, spread almost evenly across its options (evenness 0.93 against 0.57 for isoleucine). Those two families are where a codon-optimizer has the most and the least room to move.

Measured across all 59 sense codons, this table correlates most closely with M. tuberculosis (r = 1.000) and least with Ferret (r = 0.450). A sequence tuned for the first would need little adjustment to move here; one tuned for the second would need a great deal.

Relative to the average across the 26 organisms on this site, M. bovis (bovine/elephant TB) leans hardest on CCG (+0.380 against the mean) and avoids AAT most (-0.248). Those two are the codons that most distinguish this table from the others.

Preferred and avoided codons

Amino acid	Preferred	Freq	RSCU	Avoided	Freq	RSCU
Alanine A	GCC	0.447	1.79	GCT	0.082	0.33
Arginine R	CGC	0.391	2.34	AGA	0.016	0.10
Asparagine N	AAC	0.786	1.57	AAT	0.214	0.43
Aspartate D	GAC	0.726	1.45	GAT	0.274	0.55
Cysteine C	TGC	0.754	1.51	TGT	0.246	0.49
Glutamate E	GAG	0.654	1.31	GAA	0.346	0.69
Glutamine Q	CAG	0.745	1.49	CAA	0.255	0.51
Glycine G	GGC	0.501	2.00	GGA	0.105	0.42
Histidine H	CAC	0.704	1.41	CAT	0.296	0.59
Isoleucine I	ATC	0.795	2.38	ATA	0.051	0.15
Leucine L	CTG	0.518	3.11	TTA	0.017	0.10
Lysine K	AAG	0.744	1.49	AAA	0.256	0.51
Phenylalanine F	TTC	0.789	1.58	TTT	0.211	0.42
Proline P	CCG	0.537	2.15	CCT	0.063	0.25
Serine S	TCG	0.357	2.14	TCT	0.042	0.25
Threonine T	ACC	0.592	2.37	ACT	0.063	0.25
Tyrosine Y	TAC	0.707	1.41	TAT	0.293	0.59
Valine V	GTG	0.464	1.85	GTA	0.056	0.22

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCC	0.4470	1.788
	GCG	0.3729	1.492
	GCA	0.0977	0.391
	GCT	0.0823	0.329
Arginine R	CGC	0.3908	2.345
	CGG	0.3324	1.994
	CGT	0.1148	0.689
	CGA	0.0999	0.599
	AGG	0.0460	0.276
	AGA	0.0161	0.097
Asparagine N	AAC	0.7858	1.572
Asparagine N	AAT	0.2142	0.428
Aspartate D	GAC	0.7261	1.452
Aspartate D	GAT	0.2739	0.548
Cysteine C	TGC	0.7538	1.508
Cysteine C	TGT	0.2462	0.492
Glutamate E	GAG	0.6543	1.309
Glutamate E	GAA	0.3457	0.691
Glutamine Q	CAG	0.7449	1.490
Glutamine Q	CAA	0.2551	0.510
Glycine G	GGC	0.5008	2.003
	GGG	0.2009	0.804
	GGT	0.1929	0.772
	GGA	0.1054	0.422
Histidine H	CAC	0.7042	1.408
Histidine H	CAT	0.2958	0.592
Isoleucine I	ATC	0.7950	2.385
	ATT	0.1539	0.462
	ATA	0.0510	0.153
Leucine L	CTG	0.5180	3.108
	CTC	0.1793	1.076
	TTG	0.1787	1.072
	CTT	0.0598	0.359
	CTA	0.0471	0.283
	TTA	0.0171	0.103
Lysine K	AAG	0.7437	1.487
Lysine K	AAA	0.2563	0.513
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTC	0.7888	1.578
Phenylalanine F	TTT	0.2112	0.422
Proline P	CCG	0.5371	2.148
	CCC	0.2924	1.170
	CCA	0.1074	0.430
	CCT	0.0632	0.253
Serine S	TCG	0.3566	2.140
	AGC	0.2616	1.570
	TCC	0.2080	1.248
	AGT	0.0661	0.397
	TCA	0.0660	0.396
	TCT	0.0417	0.250
Threonine T	ACC	0.5923	2.369
	ACG	0.2643	1.057
	ACA	0.0805	0.322
	ACT	0.0629	0.252
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAC	0.7071	1.414
Tyrosine Y	TAT	0.2929	0.586
Valine V	GTG	0.4637	1.855
	GTC	0.3830	1.532
	GTT	0.0978	0.391
	GTA	0.0556	0.222

Provenance

Computed from 1,229 RefSeq coding sequences for Mycobacterium bovis, sampled and counted codon by codon. Frequencies are relative within each amino acid family. Page generated 2026-08-09.

The full derivation of GC3, RSCU and the effective number of codons, along with the limits of each, is set out once in the methods note rather than repeated on every page.

Use this table

Nucleora codon-optimizes a coding sequence against this table directly, then folds the result and reports where structure would interfere with expression.

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