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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.
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BMC Microbiology

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