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

Open Data