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Table 3 Percentages of the patterns for which the hypothesis of equality of “pattern region codon usage (RCU)” and “pattern gene codon usage (GCU)” is rejected, grouped by the specificity of the pattern

From: Dependency of codon usage on protein sequence patterns: a statistical study

Pattern specificity range Number of valid patterns Number of patterns with non-equal pattern region codon usage and pattern gene codon usage Percentages of patterns with non-equal pattern region codon usage and pattern gene codon usage for amino acids
[ 9-12) 12 10 %83.3
[ 12-15) 709 529 %74.6
[ 15-18) 2111 1420 %67.3
[ 18-21) 3792 2503 %66.0
[ 21-24) 3194 2112 %66.1
[ 24-27) 1516 992 %65.4
[ 27-30) 876 572 %65.3
[ 30-33) 444 282 %63.5
[ 33-36) 238 148 %62.2
[ 36-39) 184 130 %70.7
[ 39-42) 185 123 %66.5
[ 42-45) 128 69 %53.9
[ 45-48) 67 44 %65.7
[ 48-51) 57 32 %56.1
[ 51-54) 34 19 %55.9
[ 57-60) 21 7 %33.3
[ 60-63) 12 6 %50.0
  1. The range of pattern specificities are divided to subranges of length 3, and the results are provided for each range of pattern specificities. If an amino acid appears 30 times in a pattern region, and each of its codons appears at least once in this region, we consider the pattern as a valid pattern for the amino acid. The “number of patterns with non-equal pattern region codon usage and pattern gene codon usage” is the number of cases for which the hypothesis of the equality of “pattern region codon usage (RCU)” and “pattern gene codon usage (GCU)” is rejected. The “Percentages of patterns with non-equal pattern region codon usage and pattern gene codon usage for amino acids” column represents the ratio of the number of cases with non-equal codon usages to the number of valid cases. We presented the rows with at least 10 valid patterns.