Letter Based Codes
| BaseID | 2-Letter | Verbose Code |
| A | dA | dA |
| C | dC | dC |
| G | dG | dG |
| T | dT | T |
| a | rA | rA |
| c | rC | rC |
| g | rG | rG |
| U | rU | U |
| t | 3T | idT |
| 1 | mA | r2’OMeA |
| 2 | mC | r2’OMeC |
| 3 | mG | r2’OMeG |
| 4 | mU | 2’OMeU |
| 5 | As | dA-s |
| 6 | Cs | dC-s |
| 7 | Gs | dG-s |
| 8 | Ts | T-s |
| 1s | r2’OMeA-s | |
| J | 2s | r2’OMeC-s |
| K | 3s | r2’OMeG-s |
| L | 4s | 2’OMeU-s |
| B | as | rA-s |
| E | cs | rC-s |
| F | gs | rG-s |
| H | us | U-s |
| n | 6n | AminoC6 |
| i | Tn | T-C6amino |
| b | bb | BiotinC6 |
| p | pp | Phos |
| u | rU | U |
| s | ss | C6-SS-C6- |
| m | n3 | C7-amino-3′ |
| h | al | 5′-Aldehyde 4FB |
| O | BT | Biotin-TEG |
| S | 18 | Spacer18 |
| f | FA | C6FAM |
| r | TA | TAMRA |
| P | HP | HydroxyProline |
| M | fA | r2’FluoroA |
| N | fC | r2’FluoroC |
| Q | fG | r2’FluoroG |
| R | fU | 2’FluoroU |
| I | dI | dInosine |
| o | Pn | C6Amino |
| q | Bp | BiotinPEG |
| V | n5 | 5’Amino5 |
| v | Bs | Biotin-Osu |
| W | TS | T(S2) |
| X | XX | XXX |
| Y | Cy | Cy3 |
| Z | sT | dT(thiol) |
| d | dB | Biotin |
| e | 3S | C3-Thiol |
| j | 8g | (8oxo_rg) |
| k | gg | glyceryl |
| l | NT | NHS-Carboxy-dT |
| w | dN | N |
| x | Ch | Cholesterol |
| y | 5B | Biotin-C4-amide-C4 |
| z | C5 | Cy5 |
| 9 | fI | 2fluoro_dI |
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