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Table 2 Suggested forward primer regions based on HCV whole genome PWM

From: Hepatitis C virus whole genome position weight matrix and robust primer design

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    
  1. 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.