Table 1.
Codon usage and tRNA present in phage N1M2 and N1.
| Codon | N1M2 frequency % | N1 frequency % | Ratio (phage/host) | N1M2 tRNA (location) | N1 tRNA (location) | |
|---|---|---|---|---|---|---|
| Phage < Host | GCC | 0.84 | 3.29 | 0.26 | 0 | 3 (569533–569608) (569682–569758) (569832–569907) |
| GCG | 0.57 | 4.13 | 0.14 | 0 | 0 | |
| CGA | 0.29 | 0.82 | 0.35 | 0 | 0 | |
| CGC | 0.60 | 3.11 | 0.19 | 0 | 0 | |
| CGG | 0.16 | 1.62 | 0.10 | 0 | 0 | |
| AGG | 0.17 | 0.38 | 0.45 | 0 | 0 | |
| TGC | 0.24 | 1.13 | 0.21 | 0 | 0 | |
| CAG | 1.59 | 2.77 | 0.57 | 0 | 4 (295367–295451) (295480–295563) (295593–295677) (925991–926076) | |
| GGC | 0.84 | 3.84 | 0.22 | 0 | 0 | |
| GGG | 0.77 | 1.32 | 0.58 | 0 | 0 | |
| CAC | 0.74 | 1.11 | 0.67 | 0 | 0 | |
| CAT | 1.04 | 1.23 | 0.85 | 1 (249035–249111) | 0 | |
| CTC | 0.73 | 1.23 | 0.59 | 0 | 0 | |
| CTG | 2.25 | 4.95 | 0.45 | 0 | 0 | |
| CCC | 0.16 | 0.83 | 0.19 | 0 | 0 | |
| CCG | 0.55 | 3.10 | 0.18 | 0 | 1 (926231–926307) | |
| TCC | 0.81 | 1.04 | 0.78 | 0 | 0 | |
| TCG | 0.31 | 1.38 | 0.22 | 0 | 0 | |
| AGC | 0.62 | 2.08 | 0.30 | 0 | 0 | |
| ACC | 1.75 | 2.51 | 0.70 | 0 | 0 | |
| ACG | 0.44 | 1.44 | 0.31 | 0 | 0 | |
| TGG | 1.22 | 1.54 | 0.79 | 0 | 0 | |
| GTC | 0.94 | 1.74 | 0.54 | 0 | 1 (962722–962798) | |
| GTG | 0.84 | 2.31 | 0.36 | 0 | 1 (926098–926174) | |
| Phage = Host | GAC | 1.90 | 1.83 | 1.04 | 0 | 0 |
| GAG | 1.64 | 1.75 | 0.94 | 0 | 0 | |
| GGA | 0.86 | 0.86 | 1.00 | 0 | 0 | |
| CTA | 0.57 | 0.60 | 0.95 | 0 | 0 | |
| TTT | 1.88 | 2.08 | 0.90 | 0 | 0 | |
| Phage > Host | GCA | 1.77 | 1.25 | 1.42 | 0 | 0 |
| GCT | 2.92 | 1.63 | 1.79 | 0 | 0 | |
| CGT | 2.56 | 1.66 | 1.54 | 0 | 0 | |
| AGA | 0.72 | 0.39 | 1.85 | 0 | 0 | |
| AAC | 3.15 | 2.08 | 1.51 | 0 | 0 | |
| AAT | 2.68 | 1.41 | 1.90 | 0 | 0 | |
| GAT | 4.63 | 2.79 | 1.66 | 0 | 2 (786427–786503) (966444–966520) | |
| TGT | 0.62 | 0.53 | 1.17 | 0 | 1 (778986–77906) | |
| CAA | 1.79 | 1.15 | 1.56 | 0 | 2 (331627–331705) (440212–440130) | |
| GAA | 4.86 | 2.86 | 1.70 | 0 | 1 (610794–610869) | |
| GGT | 4.15 | 1.68 | 2.47 | 0 | 1 (778693–778620) | |
| ATA | 0.71 | 0.58 | 1.22 | 0 | 0 | |
| ATC | 3.32 | 2.60 | 1.28 | 0 | 0 | |
| ATT | 3.08 | 2.15 | 1.43 | 0 | 0 | |
| CTT | 1.55 | 1.01 | 1.53 | 0 | 0 | |
| TTA | 1.62 | 1.02 | 1.59 | 0 | 0 | |
| TTG | 1.45 | 1.27 | 1.14 | 0 | 1 (925945–925873) | |
| AAA | 4.40 | 2.82 | 1.56 | 0 | 0 | |
| AAG | 2.44 | 1.30 | 1.88 | 0 | 0 | |
| ATG | 2.49 | 2.16 | 1.15 | 0 | 0 | |
| TTC | 2.53 | 1.84 | 1.38 | 0 | 4 (409621–409696) (740942–741019) (778699–778773) (875919–875994) | |
| CCA | 1.58 | 0.73 | 2.16 | 0 | 1 (962668–962592) | |
| CCT | 1.83 | 0.70 | 2.61 | 0 | 0 | |
| TCA | 0.88 | 0.78 | 1.13 | 0 | 0 | |
| TCT | 2.13 | 0.73 | 2.92 | 1 (249512–249588) | 0 | |
| AGT | 1.23 | 0.58 | 2.12 | 0 | 0 | |
| ACA | 1.25 | 0.48 | 2.6 | 0 | 0 | |
| ACT | 3.02 | 0.68 | 4.44 | 0 | 0 | |
| TAC | 1.43 | 1.23 | 1.16 | 0 | 0 | |
| TAT | 2.69 | 1.50 | 1.79 | 0 | 0 | |
| GTA | 1.77 | 0.94 | 1.88 | 0 | 1 (778891–778975) | |
| GTT | 3.40 | 1.43 | 2.38 | 1 (249909–249982) | 0 |
Codon usage was determined using the University of Georgia online amino acid and codon usage statictics online tool. The presence of transfer RNA genes was determined using tRNAscan-SE and ARAGORN.