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Table 3 Suggested reverse 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
30 54 1.94 467 491 1.938 3352 3376 1.822
31 55 1.94 470 494 1.938 3630 3654 1.808
55 79 1.956 471 495 1.939 3726 3750 1.684
63 87 1.942 474 498 1.938 5043 5067 1.876
77 101 1.929 475 499 1.931 5072 5096 1.835
116 140 1.972 476 500 1.926 5209 5233 1.818
117 141 1.972 477 501 1.923 5210 5234 1.792
129 153 1.954 478 502 1.891 5221 5245 1.763
164 188 1.865 487 511 1.918 5377 5401 1.754
165 189 1.865 488 512 1.918 5378 5402 1.732
166 190 1.865 493 517 1.89 5522 5546 1.745
187 211 1.9 494 518 1.89 5659 5683 1.695
188 212 1.891 572 596 1.805 5680 5704 1.882
191 215 1.89 582 606 1.873 5695 5719 1.866
197 221 1.878 603 627 1.811 6286 6310 1.782
201 225 1.846 604 628 1.77 6325 6349 1.815
209 233 1.868 605 629 1.77 6340 6364 1.79
235 259 1.923 633 657 1.897 6341 6365 1.746
236 260 1.922 634 658 1.864 6379 6403 1.648
237 261 1.922 642 666 1.743 6454 6478 1.783
238 262 1.922 691 715 1.542 6579 6603 1.838
241 265 1.915 730 754 1.484 7120 7144 1.868
242 266 1.914 856 880 1.58 7121 7145 1.868
243 267 1.913 1297 1321 1.782 7272 7296 1.794
244 268 1.912 1320 1344 1.893 7273 7297 1.754
245 269 1.912 1325 1349 1.862 7311 7335 1.674
260 284 1.953 1326 1350 1.834 7591 7615 1.856
261 285 1.953 1425 1449 1.762 7712 7736 1.821
286 310 1.924 1426 1450 1.729 7902 7926 1.813
287 311 1.922 1439 1463 1.716 8038 8062 1.878
360 384 1.936 1470 1494 1.67 8057 8081 1.912
387 411 1.899 1471 1495 1.62 8058 8082 1.912
403 427 1.914 1777 1801 1.532 8092 8116 1.864
407 431 1.937 2534 2558 1.737 8112 8136 1.833
418 442 1.894 2715 2739 1.928 8256 8280 1.833
428 452 1.914 2769 2793 1.918 8293 8317 1.806
429 453 1.914 2770 2794 1.907 8916 8940 1.839
430 454 1.914 2771 2795 1.894 8985 9009 1.684
445 469 1.908 3270 3294 1.759 9203 9227 1.742
452 476 1.922 3331 3355 1.854 9498 9522 1.574
466 490 1.936 3351 3375 1.84    
  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.