Table 3 |
||||||||
|
Suggested reverse 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 |
|
|
||||||||
|
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 |
|||
|
|
||||||||
|
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. |
||||||||
|
Qiu et al. BMC Microbiology 2002 2:29 doi:10.1186/1471-2180-2-29 |
||||||||
