Skip to main content

Table 1 Primer sequences for amplification of BLV LTR candidate regions by the Coordination of Common Motif (CoCoMo) algorithm

From: BLV-CoCoMo-qPCR: Quantitation of bovine leukemia virus proviral load using the CoCoMo algorithm

Primer ID

Sequence

Primer annealing position in the BLV LTR sequence1

  

3'LTR

5'LTR

1

ACCTGYYGWKAAAYTAATAMAATGC

162-186

8351-8375

2

CYDKYSRGYTARCGGCRCCAGAAGC

192-216

8381-8405

3

GSCCYDKYSRGYTARCGGCRCCAGA

189-213

8378-8402

4

VRRAAWHYMMNMYCYKDAGCTGCTG

132-156

8321-8345

5

KDDWAAHTWAWWMAAWKSCGGCCCT

169-193

8358-8382

6

MNMYCYKDRSYKSYKSAYYTCACCT

141-165

8330-8354

7

YYSVRRAAWHYMMNMYCYKDAGCTG

129-153

8318-8342

8

GCTCCCGAGRCCTTCTGGTCGGCTA

266-290

8455-8479

12

NMYCYKDRSYKSYKSAYYTCACCTG

142-166

8331-8355

17

SGKYCYGAGYYYKCTTGCTCCCGAG

250-274

8439-8463

20

YSGKYCYGAGYYYKCTTGCTCCCGA

249-273

8438-8462

22

HVVRRWMHHYMMNMYSHKNWGCTGC

130-154

8319-8343

30

YYYSGKYCYGAGYYYKCTTGCTCCC

247-271

8436-8460

32

SGSMVCMRRARSBRYTCTYYTCCTG

204-228

8393-8417

33

YYYYSGKYCYGAGYYYKCTTGCTCC

246-270

8435-8459

34

VCMRRARSBRYTCTYYTCCTGAGAC

208-232

8397-8421

39

GSMVCMRRARSBRYTCTYYTCCTGA

205-229

8394-8418

56

MNMYMYDNVSYKVBBBRYYKCACCT

141-165

8330-8354

58

YSBRRGBYBKYTYKCDSCNGAGACC

253-277

8442-8466

62

BYSBRRGBYBKYTYKCDSCNGAGAC

323-347

8441-8465

63

YYYYBGBYYYSWGHYYBCKYGCTCC

246-270

8587-8611

64

VRDNYHHNHYYYBNRKYYBYTGACC

354-378

8324-8348

65

HVVNVHVNHHVVNVNSNKNWGMYGS

43-67, 68-92, 130-154

8232-56, 8257-81, 8319-43

66

NNHHDHBHRWDMMAHNSMBDSMSYK

124-148, 169-193, 170-194

8313-37, 8358-82, 8359-83

68

BNNVBBHVNVHNYYYBNYHVMYBHS

26-50, 91-115, 247-271

8215-39, 8280-8304, 8436-60

69

NVMNBNNHHVDNHWMHYSMBRMSCT

123-147, 128-152, 211-235

8312-36, 8317-41, 8400-24

70

NNNBBHVBVNNHNBBRHYYBTCTCC

202-226, 360-384, 375-399

8391-8415, 8549-73, 8564-88

73

TGGTCTCHGCYGAGARCCNCCCTCC

325-349

8514-8538

76

GCCGACCAGAAGGYCTCGGGAGCAA

264-288

8453-8477

80

SSSRKKBVVRVSCMRRMSSCCTTGG

421-445

8610-8634

81

TACCTGMCSSCTKSCGGATAGCCGA

284-308

8473-8497

83

KKBVVRVSCMRRMSSCCTTGGAGCG

417-441

8606-8630

85

GMCSSCTKSCGGATAGCCGACCAGA

279-303

8468-8492

90

CCTGMCSSCTKSCGGATAGCCGACC

282-306

8471-8495

95

YYYMMVMVBBKKNBTDKCCTTACCT

304-328

8493-8517

97

RMVVRDVBVVGVBDSMVRSCCWKRS

421-445, 429-453

8610-8634, 8618-8642

103

VMVVVDRVNVSSVDKVMRVSCYWGR

421-445, 430-454

8610-8634, 8619-8643

108

YYMMVMVBBKKNBTDKCCTTACCTG

303-327

8492-8516,

112

VVVRRNBSVRRBBVVRVSCCMKWSG

421-445, 428-452

8610-8634, 8617-8641

130

NKNVVRVSCVVVVVVVSWKRGAGCG

417-441, 484-508

8606-8630, 8673-8697

135

NNVVNDRVNVBNNDKNNNNNBHNND

4-28, 90-114, 105-129, etc

8610-8634, 8619-8643, etc

136

BHYYYBNSSSVHKVSRGRKMGCCGA

284-308, 495-519

8473-8497, 8684-8708

137

DRRRSYHVSVRDRSTCDSDRCCGAG

247-271, 336-360

8436-8460, 8525-8549

138

WWVVDSHYSSVKKSSKSWYWGCCGA

284-308, 337-861

8473-8497, 8526-8550

140

NHNNNBBBSSVVTRGWSKSHGCCGA

337-361, 495-519

8526-8550, 8684-8708

141

NRRRVBHVVVRDRSYYNSDRCCGAG

247-271, 336-360

8436-8460, 8525-8549

142

NHNNNBBBSSVNYDSWSBBNGCCGA

337-361, 495-519

8526-8550, 8684-8708

143

VMVVVNDNNVSSVDDVMVVVCYWGR

279-303, 421-445, 430-454

8468-8492, 8610-34, 8619-43

144

VVVRRNNVVRDBBVVVVBSSMKWSG

378-402, 421-445, 428-452

8567-8591, 8610-34, 8617-41

  1. 1Numbers indicate the position in the nucleotide sequence of the FLK-BLV subclone pBLV913 [DDBJ: EF600696].