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 |