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Table 3
Ranking of the 10 most rejected codon-triplets in fungal ORfeomes
	A.fum	C.alb	C.gla	D.han	E.gos	K.lac	S.bay	S.cer	S.mik	S.par	S.pom

1	GAC	GAA	GAA	GAA	GAT	GAA	AAA	GAA	GAA	AAA	GAA
	GCT	AAA	AAA	AAA	AAG	AAA	GAT	GAT	GAT	GAT	CCT
	AAG	AAA	AAG	AAA	GAG	AAA	AAG	AAG	AAG	AAG	AAA
2	GAC	AAA	AAA	AAA	GAC	GAA	GAT	AAA	AAT	ATT	GAA
	GAT	AAA	AAA	AAA	GAT	AAA	AAG	AAA	ATT	AAA	GAT
	AAG	AAT	AAG	AAA	AAG	AAG	GAA	GAA	AAA	AAA	AAA
3	GCT	AAA	GAA	GAA	GAG	AAA	GAA	GAT	ATT	GAA	AAA
	AAG	AAA	AAA	AAA	GAT	AAA	AAA	CAA	AAA	GAT	TTT
	GAC	AAA	AAA	AAT	AAG	GAA	GGT	AAA	AAA	AAG	AAA
4	GAG	TTA	GAA	AAA	GAG	AAA	GAT	AAA	AAA	TTG	ATT
	GCT	AAA	GAT	AAA	GAT	AAA	CAA	AAA	ATT	TTT	AAA
	AAG	AAA	AAG	AAT	CAG	AAG	AAA	GAT	AAA	AAA	ATT
5	GAT	CAA	GAT	AAA	AAG	AAA	AAA	GAA	GAT	AAG	GAA
	AAG	AAA	AAG	AAA	GAT	AAA	AAG	TTT	CAA	TCT	CTT
	GCC	AAA	GGT	AAG	CAG	AAA	TTG	AAA	AAA	GAA	AAA
6	GCT	GAA	AAT	GAA	GAT	GAA	GAA	AAA	ATT	AAA	ATT
	AAG	AAA	AAG	AAA	AAG	GAT	AAA	TCT	ATT	ATT	TTT
	TTC	AAT	GGT	AAG	CAG	AAA	AAA	GAA	AAA	AAA	TTT
7	GAT	AAA	AAG	GAA	AAG	GAA	GAT	GAT	AAA	GAT	GAA
	AAG	AAA	GGT	AAA	GAT	GAT	AAG	AAA	GAT	AAG	GAT
	TTC	GAA	GAT	AAC	CTG	AAG	GAT	GGT	AAG	TCT	AAG
8	ATT	TCA	AAC	CAA	TTC	GAA	GAA	AAA	GAA	GAA	GAA
	AAG	AAA	GAA	AAA	GCG	AAA	TTT	AAA	TTT	GAT	ATT
	GAG	AAA	AAA	AAA	GAG	AAT	AAG	CAA	AAG	AAA	AAA
9	GAG	TTA	AAC	AAT	GAG	GAA	AAA	AAA	AAT	ATT	ATT
	CCT	AAA	GAT	TTT	TCT	AAA	AAA	GAT	TTT	AAA	AAA
	AAG	AAT	AAG	TTA	AAG	GAT	GAT	AAT	AAA	ATT	GAT
10	GAT	CCA	GAT	GAA	TTT	GAT	AAA	AAT	AAA	AAA	TTT
	AAG	AAA	AAG	CCA	AAG	AAA	AAA	CAA	ATT	GAT	AAA
	GAG	AAA	GAA	GAT	GAG	AAA	GAA	AAA	AAT	CAA	GTT

The complete set of codon-triplets present in the 11 fungal ORFeomes studied were identified and the codon-triplet contexts were ranked according to the difference between observed and expected values (bias). This group of codon-triplets can be divided according to the presence or absence of runs of more than 5 consecutive adenosines (underlined). Interestingly, the most common feature of these strongly repressed codon triplets was the presence of an adenosine (A) at position 4 and 7 of the triplet (X₁X₂X₃-Y₄Y₅Y₆-Z₇Z₈Z₉), a feature that appears in one third of the codon-triplets shown below.
Moura et al. BMC Genomics 2007 8:444 doi:10.1186/1471-2164-8-444

Table 3