Table 2.
Suggested forward primer regions based on HCV whole genome PWM
| Primer Start | Primer End | Conservation Score | Primer Start | Primer End | Conservation Score | Primer Start | Primer End | Conservation Score |
| 7 | 31 | 1.804 | 465 | 489 | 1.936 | 5672 | 5696 | 1.821 |
| 8 | 32 | 1.805 | 470 | 494 | 1.938 | 6263 | 6287 | 1.74 |
| 32 | 56 | 1.94 | 471 | 495 | 1.939 | 6302 | 6326 | 1.775 |
| 33 | 57 | 1.94 | 559 | 583 | 1.716 | 6317 | 6341 | 1.732 |
| 40 | 64 | 1.954 | 560 | 584 | 1.736 | 6318 | 6342 | 1.734 |
| 54 | 78 | 1.957 | 580 | 604 | 1.873 | 6323 | 6347 | 1.78 |
| 93 | 117 | 1.911 | 581 | 605 | 1.873 | 6356 | 6380 | 1.786 |
| 94 | 118 | 1.912 | 582 | 606 | 1.873 | 6376 | 6400 | 1.728 |
| 106 | 130 | 1.962 | 600 | 624 | 1.89 | 6424 | 6448 | 1.744 |
| 107 | 131 | 1.962 | 610 | 634 | 1.757 | 6431 | 6455 | 1.77 |
| 141 | 165 | 1.956 | 611 | 635 | 1.779 | 6542 | 6566 | 1.736 |
| 142 | 166 | 1.956 | 612 | 636 | 1.779 | 6556 | 6580 | 1.707 |
| 143 | 167 | 1.957 | 619 | 643 | 1.798 | 6976 | 7000 | 1.708 |
| 165 | 189 | 1.865 | 707 | 731 | 1.614 | 7018 | 7042 | 1.748 |
| 168 | 192 | 1.866 | 1297 | 1321 | 1.782 | 7081 | 7105 | 1.862 |
| 178 | 202 | 1.897 | 1298 | 1322 | 1.782 | 7097 | 7121 | 1.922 |
| 204 | 228 | 1.841 | 1302 | 1326 | 1.766 | 7098 | 7122 | 1.925 |
| 212 | 236 | 1.871 | 1303 | 1327 | 1.804 | 7249 | 7273 | 1.66 |
| 213 | 237 | 1.881 | 1402 | 1426 | 1.719 | 7250 | 7274 | 1.686 |
| 214 | 238 | 1.881 | 1403 | 1427 | 1.733 | 7251 | 7275 | 1.686 |
| 215 | 239 | 1.882 | 1404 | 1428 | 1.733 | 7288 | 7312 | 1.68 |
| 218 | 242 | 1.893 | 1447 | 1471 | 1.765 | 7568 | 7592 | 1.782 |
| 219 | 243 | 1.893 | 1448 | 1472 | 1.795 | 7569 | 7593 | 1.782 |
| 220 | 244 | 1.899 | 1449 | 1473 | 1.794 | 7581 | 7605 | 1.829 |
| 221 | 245 | 1.9 | 1754 | 1778 | 1.587 | 7587 | 7611 | 1.902 |
| 222 | 246 | 1.901 | 1755 | 1779 | 1.626 | 7689 | 7713 | 1.734 |
| 225 | 249 | 1.922 | 2511 | 2535 | 1.676 | 7879 | 7903 | 1.792 |
| 237 | 261 | 1.922 | 2572 | 2596 | 1.796 | 7895 | 7919 | 1.812 |
| 238 | 262 | 1.922 | 2692 | 2716 | 1.856 | 7985 | 8009 | 1.849 |
| 263 | 287 | 1.952 | 2715 | 2739 | 1.928 | 8015 | 8039 | 1.804 |
| 264 | 288 | 1.954 | 2746 | 2770 | 1.789 | 8016 | 8040 | 1.803 |
| 337 | 361 | 1.833 | 2747 | 2771 | 1.791 | 8034 | 8058 | 1.835 |
| 345 | 369 | 1.849 | 2748 | 2772 | 1.792 | 8035 | 8059 | 1.852 |
| 351 | 375 | 1.883 | 2820 | 2844 | 1.928 | 8040 | 8064 | 1.878 |
| 364 | 388 | 1.934 | 3247 | 3271 | 1.728 | 8089 | 8113 | 1.88 |
| 381 | 405 | 1.918 | 3308 | 3332 | 1.806 | 8090 | 8114 | 1.88 |
| 387 | 411 | 1.899 | 3328 | 3352 | 1.851 | 8159 | 8183 | 1.872 |
| 395 | 419 | 1.929 | 3329 | 3353 | 1.871 | 8192 | 8216 | 1.794 |
| 405 | 429 | 1.914 | 3330 | 3354 | 1.87 | 8233 | 8257 | 1.791 |
| 406 | 430 | 1.914 | 3439 | 3463 | 1.591 | 8234 | 8258 | 1.811 |
| 407 | 431 | 1.937 | 3607 | 3631 | 1.729 | 8295 | 8319 | 1.807 |
| 408 | 432 | 1.936 | 3703 | 3727 | 1.852 | 8312 | 8336 | 1.728 |
| 422 | 446 | 1.923 | 3886 | 3910 | 1.779 | 8726 | 8750 | 1.739 |
| 443 | 467 | 1.908 | 3892 | 3916 | 1.762 | 8893 | 8917 | 1.686 |
| 444 | 468 | 1.908 | 4955 | 4979 | 1.788 | 8926 | 8950 | 1.816 |
| 447 | 471 | 1.907 | 5049 | 5073 | 1.898 | 8962 | 8986 | 1.74 |
| 448 | 472 | 1.907 | 5186 | 5210 | 1.751 | 8963 | 8987 | 1.749 |
| 451 | 475 | 1.909 | 5187 | 5211 | 1.774 | 9048 | 9072 | 1.642 |
| 452 | 476 | 1.922 | 5198 | 5222 | 1.801 | 9114 | 9138 | 1.717 |
| 453 | 477 | 1.922 | 5354 | 5378 | 1.84 | 9180 | 9204 | 1.794 |
| 454 | 478 | 1.922 | 5355 | 5379 | 1.843 | 9202 | 9226 | 1.745 |
| 455 | 479 | 1.922 | 5499 | 5523 | 1.811 | 9315 | 9339 | 1.826 |
| 456 | 480 | 1.921 | 5636 | 5660 | 1.724 | 9475 | 9499 | 1.704 |
| 464 | 488 | 1.929 | 5657 | 5681 | 1.678 |
To ensure optimal polymerization, the 3' end and the penultimate position were required to be G or C with frequencies of ≥0.98 and the upstream position, (3' -2), a G or C with a frequency of ≥0.90 or alternatively an A or T with a frequency of ≥0.95.