Table 1 Genome-wide preferred synonymous codon usage in *S. purpuratus* | Second Base^{a} |
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| U | C | A | G |
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First Base | Codon | ρ^{b} | *P*-Value | Codon | ρ | *P*-Value | Codon | ρ | *P*-Value | Codon | ρ | *P*-Value |
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U | UUU (F) | 0.381 | 7.54E-160 | UCU (S) | 0.191 | 3.94E-39 | UAU (Y) | 0.387 | 9.07E-165 | **UGU (C)** | **-0.191** | **2.13E-39** |

**UUC (F)** | **-0.382** | **1.43E-160** | **UCC (S)** | **-0.279** | **2.19E-83** | **UAC (Y)** | **-0.381** | **1.12E-159** | UGC (C) | 0.208 | 2.18E-46 |

UUA (L) | 0.453 | 2.16E-232 | UCA (S) | 0.231 | 5.12E-57 | UAA (X) | | | UGA (X) | | |

UUG (L) | 0.274 | 1.67E-80 | UCG (S) | −0.022 | 1.27E-01 | UAG (X) | | | UGG (W) | | |

C | CUU (L) | 0.208 | 2.28E-46 | CCU (P) | 0.157 | 7.61E-27 | CAU (H) | 0.242 | 2.24E-62 | CGU (R) | −0.021 | 1.46E-01 |

**CUC (L)** | **-0.461** | **2.87E-242** | CCA (P) | 0.185 | 5.08E-37 | **CAC (H)** | **-0.228** | **1.10E-55** | **CGC (R)** | **-0.213** | **8.89E-49** |

CUA (L) | 0.253 | 1.65E-68 | **CCC (P)** | **-0.317** | **1.19E-108** | CAA (Q) | 0.382 | 1.73E-160 | CGA (R) | 0.152 | 3.05E-25 |

CUG (L) | −0.390 | 2.64E-167 | CCG (P) | −0.011 | 4.64E-01 | **CAG (Q)** | **-0.378** | **2.78E-157** | CGG (R) | 0.062 | 2.56E-05 |

A | AUU (I) | 0.342 | 3.55E-127 | ACU (T) | 0.277 | 3.53E-82 | AAU (N) | 0.454 | 2.42E-233 | AGU (S) | 0.204 | 1.68E-44 |

**AUC (I)** | **-0.536** | **1.00E-223** | **ACC (T)** | **-0.420** | **6.96E-197** | AAC (N) | **-0.452** | **5.70E-232** | AGC (S) | −0.230 | 1.61E-56 |

AUA (I) | 0.385 | 6.16E-163 | ACA (T) | 0.284 | 2.66E-86 | AAA (K) | 0.466 | 2.95E-248 | AGA (R) | 0.302 | 4.55E-98 |

AUG (M) | | | ACG (T) | −0.039 | 7.81E-03 | **AAG (K)** | **-0.467** | **1.36E-248** | AGG (R) | −0.179 | 1.90E-34 |

G | GUU (V) | 0.346 | 4.56E-130 | GCU (A) | 0.132 | 1.55E-19 | GAU (D) | 0.338 | 3.48E-124 | GGU (G) | 0.052 | 3.99E-04 |

**GUC (V)** | **-0.394** | **4.42E-171** | **GCC (A)** | **-0.441** | **9.31E-219** | **GAC (D)** | **-0.337** | **2.06E-123** | **GGC (G)** | **-0.249** | **2.88E-66** |

GUA (V) | 0.309 | 1.48E-102 | GCA (A) | 0.311 | 1.99E-104 | GAA (E) | 0.416 | 6.46E-193 | GGA (G) | 0.150 | 1.44E-24 |

GUG (V) | −0.095 | 1.17E-10 | GCG (A) | 0.045 | 2.14E-03 | **GAG (E)** | **-0.416** | 2.82E-193 | GGG (G) | 0.072 | 1.03E-06 |