Search for the best oligonucleotides according to the degree of conservation in specific sequence alignments


The table describes for each oligonucleotide different measures of sequence conservation for all sequence alignments used the database:
-PIS: percentage of identical sites
-3'PIS: percentage of identical sites in the last five nucleotides at the 3' end of oligonucleotide
-PPI: percentage of pairwise identity
-POS: Position in alignment.

HIVoligoDB_alig02
Database reference Techniques Target Original name Target length Amplicon length Sequence (5'-3') Position in reference genome Genomic region Sequence in reference genome POS Number of sequences in Alig02 PIS 3'PIS PPI Score Related publications
Database reference Techniques Target Original name Target length Amplicon length Sequence (5'-3') Position in reference genome Genomic region Sequence in reference genome POS Number of sequences in Alig02 PIS 3'PIS PPI Score Related publications
HIV2ID0001 PCR PCR primer forward SR74 21 392 GGGAGATGGGCGCGAGAAACT 541-561 gag GGGAGATGGGCGCGAGAAACT 1210-1231 95 63.64 40 94.99 66.21 6
HIV2ID0002 PCR PCR primer reverse SR75 25 GCTAGGTGGTGCTGTTGGTCTACTT 908-932 gag AAGTAGACCAACAGCACCATCTAGC 1578-1602 95 24 20 90.4 44.80 6
HIV2ID0003 Multiplex real-time PCR & mole(...) PCR primer forward SR64, envF 23 106 CTCCAGGCAAGAGTCACTGCTAT 7869-7891 env CTCCAGGCAAGAGTCACTGCTAT 8869-8891 95 69.57 80 91.75 80.44 14; 33;
HIV2ID0004 Multiplex real-time PCR & mole(...) PCR primer reverse SR65, envR 23 CCCATGGTACAGTAGTGTGGCAG 7952-7974 env CTGCCACACTACTGTACCATGGG 8952-8973 95 45.45 40 94.45 59.97 14; 33;
HIV2ID0005 PCR Probe SR76 25 TAATACTGTCTGCGTCATTTGGTGC 782-806 gag TAATACTGTCTGCGTCATTTGGTGC 1452-1476 95 36 20 92.85 49.62 33
HIV2ID0006 SYBR Green real time PCR PCR primer forward NP84 22 153 GTAGACCAACAGCACCACCTAG 910-931 gag GTAGACCAACAGCACCATCTAG 1580-1601 95 27.27 40 91.95 53.07 19
HIV2ID0007 SYBR Green real time PCR PCR primer reverse NP85 20 CTGGCACTACTTCTGCCCCG 1043-1062 gag CGGGGCAGAAGTAGTGCCAG 1716-1735 95 50 60 91.28 67.09 19
HIV2ID0008 SYBR Green real time PCR PCR primer forward NP86 22 138 GGGCAGAACAAACAGACCCAGC 1465-1486 gag GGGCAGAACAAACAGATCCAGC 2144-2165 95 50 20 87.37 52.46 19
HIV2ID0009 SYBR Green real time PCR PCR primer reverse NP87 22 GGCAGGCGGTTAGCATCTCTTC 1581-1602 gag GAAGAGATGCTGACCGCCTGTC 2260-2281 95 54.55 60 86.47 67.01 19
HIV2ID0010 SYBR Green real time PCR PCR primer forward NP76 23 211 CTCGCCTCTTGAYCGGRCTATAC 8933-8955 env GGGGGGGACTGGAAGGGATGTTT 9983-10005 95 47.83 40 94.15 60.66 19
HIV2ID0011 SYBR Green real time PCR PCR primer reverse NP77 22 CCCGCAAGAGTCTCTCTCGTAG 8602-8623 env CTACAAGAGAGACTCTTGCGGG 9635-9656 95 27.27 0 84.24 37.17 19
HIV2ID0012 Reverse Transcription�Loop-M(...) Primer forward A-F3 21 CCTTACAATCCACAAAGCCAA 4481-4501 pol CCTTACAATCCACAGAGCCAA 5260-5280 95 61.9 60 86.49 69.46 34
HIV2ID0013 Reverse Transcription�Loop-M(...) Primer reverse A-B3 23 ATTGTATTTCTTGTTCTGTGGTG 4657-4679 pol AATCAATATGATCACCACAGAAC 5436-5458 95 52.17 40 88.33 60.17 34
HIV2ID0014 Reverse Transcription�Loop-M(...) Primer forward A-Loop F 18 ACTTATCTGATTTTTTAG 6562-6579 env AGATAAGTGAGGATACTC 7451-7468 95 0 0 62.43 20.81 34
HIV2ID0015 Reverse Transcription�Loop-M(...) Primer reverse A-Loop B 21 AATTTTAAAAGAAGGGGAGGA 4607-4627 pol AATTTTAAAAGAAGGGGGGGA 5386-5406 95 85.71 100 99.7 95.14 34
HIV2ID0016 Probe S65GAG2 23 TAGGTTACGGCCCGGCGGAAAGA 602-624 gag CAGGTTACGGCCCGGCGGAAAGA 1272-1294 95 39.13 40 88.61 55.91
HIV2ID0017 Reverse transcriptase PCR Primer forward Seq.ID.NO.19 26 CCTCAATTCTCTCTTTGGAAAAGACC 2084-2109 gag CCTCAATTCTCTCTTTGGAAAAGACC 2853-2878 95 73.08 80 95.66 82.91 35
HIV2ID0018 Reverse transcriptase PCR Primer reverse Seq.ID.NO.20 26 AAATGTTGATTGGGGTATCTCCTGTC 2311-2336 pol GACAGGCGACACCCCAATCAACATTT 3081-3106 95 65.38 80 88.89 78.09 35
HIV2ID0019 Reverse transcriptase PCR Probe Seq.ID.NO.21 17 CCAAAAATAGTAGGGGG 2213-2229 ? CCAAAAATAGTAGGGGG 2983-2999 95 47.06 60 92.73 66.60 35
HIV2ID0020 Reverse transcriptase PCR Probe Seq.ID.NO.22 17 ATAGTAGCAGGAATAGA 2177-2193 ? ATAGTAGCAGGAATAGA 2947-2963 95 52.94 40 89.47 60.80 35
HIV2ID0021 Reverse transcriptase PCR Primer forward Seq.ID.NO.23 25 CAATAGTAGCAGGAATAGAGTTAGG 2175-2199 ? CAATAGTAGCAGGAATAGAGTTAGG 2945-2969 95 48 40 87.32 58.44 35
HIV2ID0022 Reverse transcriptase PCR Primer forward Seq.ID.NO.16 33 ACTGATGGCAGTTCATTGCATGAATTTTAA(...) 4585-4617 pol ACTAATGGCAATTCATTGCATGAATTTTAA(...) 5364-5396 95 60.61 60 94.22 71.61 35
HIV2ID0023 Reverse transcriptase PCR Probe Seq.ID.NO.18 20 CAGAACAAGAAATACAATTC 4674-4693 pol CAGAACAAGAGATACAATTC 5453-5472 95 50 40 93.92 61.31 35
HIV2ID0024 Reverse transcriptase PCR Primer reverse Seq.ID.NO.17 27 TTCCACAGCTGATCTCTGCCTTCTCTG 4738-4764 pol CAGAGAAGGCAGAGATCAGTTGTGGAA 5517-5543 95 62.96 80 94.38 79.11 35
HIV2ID0025 Taqman real-time PCR Primer forward HIV-2TMfpr1 20 81 AACAAACCACGACGGAGTGC 379-398 ? AACAAACCACGACGGAGTGC 1022-1041 88 25 40 93.19 52.73 36
HIV2ID0026 Taqman real-time PCR Primer reverse HIV-2TMrpr1 19 CCACACGCTGCCTTTGGTA 422-440 ? TACCAAAGGCAGCGTGTGG 1071-1090 89 25 20 90.05 45.02 36
HIV2ID0027 Taqman real-time PCR Probe Tmprobe 1 20 TCGGCCCGCGCITTTCTAGG 400-419 ? CCTAGAAAGGCGCGGGCCGA 1043-1055 88 30.77 40 90.02 53.60 36
HIV2ID0028 Taqman real-time PCR Primer forward HIV-2TMfpr2 19 67 GGCTGCACGCCCTATGATA 1083-1101 gag GGCTGCACGCCCTATGATA 1756-1774 95 52.63 40 86.08 59.57 36
HIV2ID0029 Taqman real-time PCR Primer reverse HIV-2TMrpr2 19 TCTGCATGGCTGCTTGATG 1131-1149 gag CATCAAGCAGCCATGCAGA 1804-1822 95 68.42 80 88.29 78.90 36
HIV2ID0030 Taqman real-time PCR Probe Tmprobe 2.1 27 TCGCCCACACAATTAAGCATTTGGTTG 1103-1129 gag CAACCAAATGCTTAATTGTGTGGGCGA 1776-1802 95 62.96 80 88.66 77.21 36
HIV2ID0031 Taqman real-time PCR Probe Tmprobe 2.2 27 TCGCCCACACAATTAAGCATTTGATTA 1103-1129 gag CAACCAAATGCTTAATTGTGTGGGCGA 1776-1802 95 62.96 80 88.66 77.21 36
HIV2ID0032 Taqman real-time PCR Primer forward HIV-2TM1sfpr 21 355 CGCCTGGTCATTCGGTGTTCA 207-227 LTR CGCCTGGTCATTCGGTGTTCA 823-844 65 0 0 82.05 27.35 36
HIV2ID0033 Taqman real-time PCR Primer reverse HIV-2TM1srpr 20 AGTTTCTCGCGCCCATCTCC 542-561 gag GGAGATGGGCGCGAGAAACT 1211-1231 95 61.9 60 94.74 72.21 36
HIV2ID0034 Taqman real-time PCR Primer forward HIV-2TM2sfpr 19 417 AGGAACTGCAGAGAAAATG 881-899 gag AGGAACTGCAGAGAAAATG 1551-1569 95 0 0 80.63 26.88 36
HIV2ID0035 Taqman real-time PCR Primer reverse HIV-2TM2srpr 24 GTGCTTGTTGTCCCTGCTATGTCA 1250-1273 gag TGACATAGCAGGGACAACAAGCAC 1929-1952 95 62.5 60 84.08 68.86 36
HIV2ID0036 Long PCR (XL PCR) and nested P(...) Primer forward LTR1 22 TTCCCTGCTRGACTCTCACCAG 75-96 LTR TTCCCTGCTAGACTCTCACCAG 684-705 47 45.45 40 97.21 60.89 37
HIV2ID0037 Long PCR (XL PCR) and nested P(...) Primer reverse LTR2 19 ACATCCCTTCCAGTCCCCC 8935-8953 LTR GGGGGACTGGAAGGGATGT 9985-10003 95 57.89 40 96.12 64.67 37
HIV2ID0038 Long PCR (XL PCR) and nested P(...) Primer forward ENVF 27 TATAGGCCWGTTTTCTCTTCCCCYCCC 8265-8291 env TATAGGCCTGTTTTCTCTTCCCCCCCC 9277-9303 95 51.85 20 91.57 54.47 37
HIV2ID0039 Nested PCR Primer forward GAGOG AS1 20 TTCAGGCACTCTCAGAAGGC 1066-1085 gag TTCAGGCACTCTCAGAAGGC 1739-1758 95 60 60 88.91 69.64 38
HIV2ID0040 Long PCR (XL PCR) and nested P(...) Primer forward EB0 25 ATACAGTGCTTRCCAGACAATGATG 6300-6324 env ATACAGTGCTTGCCTGACAATGATG 7141-7165 95 48 60 84.51 64.17 37
HIV2ID0041 Long PCR (XL PCR) and nested P(...) Primer reverse EB6 20 CCATTRAAGCCAAACCAWGT 6945-6964 env ACATGGTTTGGCTTTAATGG 7861-7880 95 70 80 93.95 81.32 37
HIV2ID0042 Long PCR (XL PCR) and nested P(...) Primer forward EB2 22 TCATGTGAYAARCAYTATTGGG 6783-6804 env TCATGTGACAAGCACTATTGGG 7699-7720 95 63.64 80 91.16 78.27 37
HIV2ID0043 Long PCR (XL PCR) and nested P(...) Primer reverse EB5 20 CTCCTCTGCAGTTAGTCCAC 7310-7329 env GTGGACTAACTGCAGAGGAG 8247-8266 95 70 80 91.83 80.61 37
HIV2ID0044 Long PCR (XL PCR) and nested P(...) Primer forward EB7 17 CCYAGGCAAGCATGGTG 7149-7165 env CCCAGACAAGCATGGTG 8068-8084 95 64.71 100 85.7 83.47 37
HIV2ID0045 Long PCR (XL PCR) and nested P(...) Primer reverse ENVE 20 GCACATCCCCATGAATTTAG 7920-7939 env CTAAATTCATGGGGATGTGC 8920-8939 95 60 40 91.45 63.82 37
HIV2ID0046 Nested PCR Primer forward ENVA 33 GCTAGGGTTCTTGGGTTTTCTCGCRACAGC(...) 7691-7723 env GCTAGGGTTCTTGGGTTTTCTCGCAACAGC(...) 8688-8720 95 45.45 80 93 72.82 39
HIV2ID0047 Nested PCR Primer reverse ENVB 30 CAAGAGGCGTATCAGCTGGCGGATCAGGAA 8415-8444 env TTCCTGATCCGCCAGCTGATTCGCCTCTTG 9427-9456 95 33.33 40 87.3 53.54 39
HIV2ID0048 Long PCR (XL PCR) and nested P(...) Primer reverse ENVG 24 CTTCTTGGATCCACTCGCACCCAT 8557-8580 env ATGGGTGCGAGTGGATCCAAGAAG 9590-9613 95 37.5 100 77.59 71.70 37
HIV2ID0049 Nested PCR Primer forward LTR9432 22 AGGAGCTGGTGGGGAACGCCCT 9432-9453 LTR AGGAGCTGGTGGGGAACGCCCT 10539-10559 75 33.33 60 82.35 58.56 40
HIV2ID0050 Nested PCR Primer reverse GAG OG S1 INV 23 AGTTTCTCGCGCCCATCTCCCAC 539-561 gag GTGGGAGATGGGCGCGAGAAACT 1208-1231 95 62.5 80 95.33 79.28 40
HIV2ID0051 Nested PCR Primer forward GAG OG S1 23 GTGGGAGATGGGCGCGAGAAACT 539-561 gag GTGGGAGATGGGCGCGAGAAACT 1208-1231 95 62.5 40 95.33 65.94 38
HIV2ID0052 Nested PCR Primer reverse GAG OG AS1 24 GGATTTCAGGCACTCTCAGAAGGC 1062-1085 gag GGATTTCAGGCACTCTCAGAAGGC 1735-1758 95 58.33 60 90 69.44 38
HIV2ID0053 Nested PCR Primer forward GAGOG AS1 INV RAC 24 CCAGGATTTCAGGCACTCTCAGAG 1059-1082 gag CCAGGATTTCAGGCACTCTCAGAA 1732-1755 95 54.17 60 92.11 68.76 40
HIV2ID0054 Nested PCR Primer reverse RTC DR INV 20 GATTGGGGTGTCTCCTGTCA 2310-2329 pol TGACAGGCGACACCCCAATC 3080-3099 95 65 80 88.25 77.75 40
HIV2ID0055 Nested PCR Primer forward X410 21 CACCTCAATTCTCTCTTTGGA 2082-2102 gag CACCTCAATTCTCTCTTTGGA 2851-2871 95 80.95 60 99.31 80.09 40
HIV2ID0056 Nested PCR Primer reverse RT4 30 TCCCCAAATGACTAGTGCTTCTTTTCCTAT 3500-3529 pol ATAGGAAAAGAAGCACTAGTCATTTGGGGA 4276-4305 95 43.33 60 90.01 64.45 39
HIV2ID0057 Nested PCR Primer reverse PFD INV 21 CTGCCTTCTCTGAAATAGACC 4729-4749 pol GGTCTATTTCAGAGAAGGCAG 5508-5528 95 76.19 80 97.93 84.71 40
HIV2ID0058 Nested PCR Primer forward RT SEQ1 21 GGATGGGCTATGAACTATGGC 3066-3086 pol GGATGGGCTATGAACTATGGC 3839-3859 95 47.62 40 87.93 58.52 40
HIV2ID0059 Nested PCR Primer forward POL OG 450 23 GGAGTAGTAGAAGCAATGAATCA 4502-4524 pol GGAGTAGTAGAAGCAATGAATCA 5281-5303 95 52.17 20 92.48 54.88 38
HIV2ID0060 Nested PCR Primer reverse POL OG 479 23 CCTACCTTGACTAGGACTGCTCC 4796-4818 pol GGAGCAGTCCTAGTCAAGGTAGG 5575-5597 95 69.57 80 92.89 80.82 38
HIV2ID0061 Nested PCR Primer forward POL OG 479 INV 23 GGAGCAGTCCTAGTCAAGGTAGG 4796-4818 pol GGAGCAGTCCTAGTCAAGGTAGG 5575-5597 95 69.57 100 92.89 87.49 38
HIV2ID0062 Nested PCR Primer reverse DR TAT1 20 TTGAGTGCCGACATCCCCCT 5915-5934 tat AGCAGGATGTGGCCACTCAA 6735-6754 95 20 20 74.83 38.28 40
HIV2ID0063 Nested PCR Primer forward ENV4 24 AGTAACAGAGCAAGCAGTGGAAGA 6380-6403 env AGTAACAGAACAAGCAATAGAAGA 7221-7244 95 45.83 40 91.24 59.02 40
HIV2ID0064 Nested PCR Primer reverse SLTR5 24 ACCTGCTAGTGCTGGAGAGAACCT 39-62 LTR AGGTTCTCTCCAGCACTAGCAGGT 648-671 46 37.5 20 97.64 51.71 40
HIV2ID0065 Nested PCR Primer reverse LTR 9574 19 TGGTGAGAGTCTAGCAGGG 9574-9592 LTR CCCTGCTAGACTCTCACCA 10682-10701 46 55 0 97.24 50.75 41