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.

EbolaID_alig01
Database reference Target Original name Sequence (5-3) Position in reference genome Genomic region Sequence in reference genome POS PIS 3'PIS PPI Related publication
Database reference Target Original name Sequence (5-3) Position in reference genome Genomic region Sequence in reference genome POS PIS 3'PIS PPI Related publication
EBOLAID001
Raw data
Min-max 		PCR primer forward EBO-1 TGGGTAATYATCCTYTTCCA 6102-6121 GP UGGGUAAUUAUCCUUUUCCA 7521-7540 20 40 75.06 1
EBOLAID002
Raw data
Min-max 		PCR primer reverse EBO-2 ACGACACCTTCAGCRAAAGT 6561-6580 GP ACUUUCGCUGAAGGUGUCGU 7996-8015 25 0 74.37 1
EBOLAID003
Raw data
Min-max 		PCR primer forward EBO-3 GTTTGTCGKGACAAACTGTC 6192-6211 GP GUUUGUCGUGACAAACUGUC 7624-7638 6.67 0 74.06 1
EBOLAID004
Raw data
Min-max 		PCR primer reverse EBO-4 TGGAARGCWAAGTCWCCGG 6481-6499 GP CCGGAGACUUUGCCUUCCA 7916-7934 31.58 20 74.82 1
EBOLAID005
Raw data
Min-max 		PCR primer forward GAB-1 GAATGTAGGTAGAACCTTCGG 13251-13271 L GAAUGUAGGUAGAACCUUCGG 16216-16236 38.1 40 73.99 1
EBOLAID006
Raw data
Min-max 		PCR primer reverse GAB-2 GCATATAACACTGTGGGATTG 13583-13603 L CAAUCCCACAGUGUUAUAUGC 16554-16574 38.1 20 78.81 1
EBOLAID007
Raw data
Min-max 		PCR primer forward EBO-BP1 AATGGGCTGAAAATTGCTACAATC 6346-6369 GP AAUGGGCUGAAAACUGCUACAAUC 7781-7804 37.5 40 86.39 2
EBOLAID008
Raw data
Min-max 		PCR primer reverse EBO-GP2 TTTTTTTAGTTTCCCAGAAGGCCCACT 6898-6924 GP AGUGGGCCUUCUGGGAAACUAAAAAAA 8370-8396 7.41 60 87.57 2
EBOLAID009
Raw data
Min-max 		PCR primer forward ZAI-NP1 GGACCGCCAAGGTAAAAAATGA 1275-1296 NP GGACCGCCAAGGUAAAAAAUGA 1415-1436 50 80 81.12 2
EBOLAID010
Raw data
Min-max 		PCR primer reverse ZAI-NP2 GCATATTGTTGGAGTTGCTTCTCAGC 1517-1542 NP GCUGAGAAGCAACUCCAACAAUAUGC 1657-1682 26.92 80 85.94 2
EBOLAID011
Raw data
Min-max 		PCR primer forward ATCGGAATTTTCTTTCTCATTGAAAGA 13214-13241 L AUCGGAACUUUUCUUUCUCAUUGAAAGA 16179-16206 35.71 80 74.35 3;4
EBOLAID012
Raw data
Min-max 		PCR primer reverse ATGTGGTGGATTATAATAATCACTGACATG(...) 13600-13632 L AUGCAUGUCAGUGAUUAUUAUAAUCCACCA(...) 16571-16603 48.48 60 81.07 3;4
EBOLAID013
Raw data
Min-max 		PCR primer forward EBOGP-1Df TGGGCTGAAAAYTGCTACAATC 6348-6369 GP UGGGCUGAAAACUGCUACAAUC 7783-7804 36.36 40 85.91 5
EBOLAID014
Raw data
Min-max 		PCR primer reverse EBOGP-1Dr CTTTGTGMACATASCGGCAC 6440-6459 GP GUGCCGGUAUGUGCACAAAG 7875-7894 20 20 80.58 5
EBOLAID015
Raw data
Min-max 		Probe EBOGP-1DZPrb CTACCAGCAGCGCCAGACGG 6402-6421 GP CUACCAGCAGCGCCAGACGG 7837-7856 15 0 75.55 5
EBOLAID016
Raw data
Min-max 		PCR primer forward FILO-A ATCGGAATTTTTCTTTCTCATT 13214-13235 L AUCGGAACUUUUCUUUCUCAUU 16179-16200 27.27 20 70.93 2;1;5;6
EBOLAID017
Raw data
Min-max 		PCR primer reverse FILO-B ATGTGGTGGGTTATAATAATCACTGACATG 13603-13632 L CAUGUCAGUGAUUAUUAUAAUCCACCACAU 16574-16603 50 60 80.93 2;1;5;6;7
EBOLAID018
Raw data
Min-max 		PCR primer forward EBOORF UP ATGGATTCTCGTCCTCAGAAAAT 470-492 NP AUGGAUUCUCGUCCUCAGAAAAU 588-612 12 0 62.49 8
EBOLAID019
Raw data
Min-max 		PCR primer reverse EBOORF DP TCACTGATGATGTTGCAGGATT 2668-2689 NP AAUCCUGCAACAUCAUCAGUGA 3103-3113 18.18 0 75.33 8
EBOLAID020
Raw data
Min-max 		PCR primer forward ENZ FP ATGATGGAAGCTACGGCG 1854-1871 NP AUGAUGGAAGCUACGGCG 2005-2022 11.11 0 62.19 8
EBOLAID021
Raw data
Min-max 		PCR primer reverse ENZ RP AGGACCAAGTCATCTGGTGC 1904-1923 NP GCACCAGAUGACUUGGUCCU 2061-2075 20 0 69.65 8
EBOLAID022
Raw data
Min-max 		Probe ENZ P CCAGAGTTACTCGGAAAACGGCATG 1876-1900 NP CCAGAGUUACUCGGAAAACGGCAUG 2027-2048 0 0 57.59 8
EBOLAID023
Raw data
Min-max 		PCR primer forward SudZaiNP1(+) GAGACAACGGAAGCTAATGC 890-909 NP GAGACAACUGAAGCUAAUGC 1030-1049 15 0 87.96 9
EBOLAID024
Raw data
Min-max 		PCR primer reverse SudZaiNP1(-) AACGGAAGATCACCATCATG 1057-1076 NP CAUGAUGGUGAUUUUCCGUU 1197-1216 30 60 74.77 9
EBOLAID025
Raw data
Min-max 		PCR primer forward SudZaiNP2(+) GGTCAGTTTCTATCCTTTGC 911-930 NP GGUCAGUUUCUCUCCUUUGC 1051-1070 20 0 72.73 9
EBOLAID026
Raw data
Min-max 		PCR primer reverse SudZaiNP2(-) CATGTGTCCAACTGATTGCC 1041-1060 NP GGCAAUCAGUAGGACACAUG 1181-1200 50 60 88.38 9
EBOLAID027
Raw data
Min-max 		PCR primer forward EBsp5 TTYCCTAGCAAYATGATGG 13345-13363 L UUUCCUAGCAAUAUGAUGG 16310-16328 57.89 80 81.05 10;4
EBOLAID028
Raw data
Min-max 		PCR primer reverse EBsp3 TATAATAATCACTGACATGCAT 13600-13621 L AUGCAUGUCAGUGAUUAUUAUA 16571-16592 45.45 60 81.54 10;4
EBOLAID029
Raw data
Min-max 		PCR primer forward evR3 TCTTGCAAGGACCGCCAAGGTAAAAA 1267-1292 NP UCUUGCAAGGACCGCCAAGGUAAAAA 1407-1432 34.62 20 74.04 11
EBOLAID030
Raw data
Min-max 		PCR primer reverse evF3 TTCAAAAGTCGGGCGAAAGGAGCATA 1346-1371 NP UAUGCUCCUUUCGCCCGACUUUUGAA 1486-1511 42.31 60 73.47 11
EBOLAID031
Raw data
Min-max 		PCR primer forward F3 AATAACGAAAGGAGTCCCTA 18338-18357 3'UTR AAUAACGAAAGGAGUCCCUA 21921-21936 0 0 65.61 12
EBOLAID032
Raw data
Min-max 		PCR primer reverse B3 TTGTATCAATATCCTGTCAG 18532-18551 3'UTR UUGUAUCAAUAUCCUGUCAG 22147-22166 0 0 63.24 12
EBOLAID033
Raw data
Min-max 		PCR primer forward Ebola-1F GATGCAGTATTCGAGCCTAATGTTCTAG 13063-13090 L GAUGCAGUAUUCGAGCCUAAUGUUCUAG 16028-16055 28.57 20 76.91 13
EBOLAID034
Raw data
Min-max 		PCR primer reverse Ebola-1R GTGTTTGAACATTGCGAGTCGGATAAG 13280-13306 L CUUAUCCGACUCGCAAUGUUCAAACAC 16245-16271 40.74 40 75.98 13
EBOLAID035
Raw data
Min-max 		Probe Ebola-P ACTCGAGTATCTACTACCACAATATCGGAA(...) 13191-13221 L ACUCGAGUAUCUACUACCACAAUAUCGGAA(...) 16156-16186 22.58 60 70.65 13
EBOLAID036
Raw data
Min-max 		PCR primer forward FiloA2.4 AAGCATTTCCTAGCAATATGATGGT 13340-13364 L AAGCAUUUCCUAGCAAUAUGAUGGU 16305-16329 56 60 81.14 7
EBOLAID037
Raw data
Min-max 		PCR primer forward FiloA2.2 AAGCCTTTCCTAGCAACATGATGGT 13340-13364 L AAGCAUUUCCUAGCAAUAUGAUGGU 16305-16329 56 60 81.14 7
EBOLAID038
Raw data
Min-max 		PCR primer forward FiloA2.3 AAGCATTCCCTAGCAACATGATGGT 13340-13364 L AAGCAUUUCCUAGCAAUAUGAUGGU 16305-16329 56 60 81.14 7
EBOLAID039
Raw data
Min-max 		PCR primer reverse FILO B-Ra GTGAGGAGGGCTATAAAAGTCACTGACATG 13603-13632 L CAUGUCAGUGAUUAUUAUAAUCCACCACAU 16574-16592 47.37 60 81.4 7
EBOLAID040
Raw data
Min-max 		Probe (FAM & BlackHole Quenche(...) FAMEBOSu CCGAAATCATCACTIGTITGGTGCCA 13411-13436 L UGGCACCACACAAGUGAUGAUUUUGG 16394-16404 18.18 0 82.09 7
EBOLAID041
Raw data
Min-max 		Probe (FAM & BlackHole Quenche(...) FAMEBOg CCAAAATCATCACTIGTGTGGTGCCA 13411-13436 L UGGCACCACACAAGUGAUGAUUUUGG 16394-16407 28.57 40 81.12 7
EBOLAID042
Raw data
Min-max 		Probe (FAM & BlackHole Quenche(...) FAMMBG CCTATGCTTGCTGAATTGTGGTGCCA 13411-13436 L UGGCACCACACAAGUGAUGAUUUUGG 16376-16385 60 40 91.4 7
EBOLAID043
Raw data
Min-max 		PCR primer forward F565 TCTGACATGGATTACCACAAGATC 518-541 NP UCUGACAUGGAUUACCACAAGAUC 638-661 20.83 20 70.24 14
EBOLAID044
Raw data
Min-max 		PCR primer reverse R640 GGATGACTCTTTGCCGAACAATC 571-593 NP GAUUGUUCGGCAAAGAGUCAUCC 691-713 17.39 20 73.76 14
EBOLAID045
Raw data
Min-max 		Probe (FAM&MGB) p597S AGGTCTGTCCGTTCAA 550-565 NP AGGUCUGUCCGUUCAA 670-685 31.25 40 72.22 14
EBOLAID046
Raw data
Min-max 		PCR primer forward F2000 TTTTCAATCCTCAACCGTAAGGC 7781-7803 GP UUUUCAAUCCUCAACCGUAAGGC 9482-9504 30.43 60 70.88 14
EBOLAID047
Raw data
Min-max 		PCR primer reverse R2079 CAGTCCGGTCCCAGAATGTG 7841-7860 GP CACAUUCUGGGACCGGACUG 9542-9561 25 0 70.62 14
EBOLAID048
Raw data
Min-max 		Probe (FAM&TAMRA) p2058A CATGTGCCGCCCCATCGCTGC 7819-7839 GP GCAGCGAUGGGGCGGCACAUG 9520-9540 47.62 60 81.5 14
EBOLAID049
Raw data
Min-max 		PCR primer forward PanFilo-L1 ATMGRAAYTTTTCYTTYTCWYT 13214-13235 L AUCGGAACUUUUCUUUCUCAUU 16179-16197 31.58 20 72.79 15
EBOLAID050
Raw data
Min-max 		PCR primer reverse Pan?lo-L2 TGWGGHGGRYTATAAWARTCACTDACAT 13604-13631 L AUGUCAGUGAUUAUUAUAAUCCACCACA 16575-16602 50 40 81.34 15
EBOLAID051
Raw data
Min-max 		PCR primer forward PanFilo-L3 GCNAARGCMTTYCCHAGYAAYATGATGG 13336-13363 L GCUAAAGCAUUUCCUAGCAAUAUGAUGG 16304-16328 60 80 82.58 15
EBOLAID052
Raw data
Min-max 		PCR primer reverse Pan?lo-L4 ATAAWARTCACTDACATGCATRTARCA 13594-13620 L UGUUAUAUGCAUGUCAGUGAUUAUUAU 16565-16591 40.74 40 78.82 15
EBOLAID053
Raw data
Min-max 		PCR primer forward KGH-F GTCGTTCCAACAATCGAGCG 10243-10262 VP24 GUCGUUCCAACAAUCGAGCG 12842-12861 0 0 67.27 16
EBOLAID054
Raw data
Min-max 		PCR primer forward KGH-R CGTCCCGTAGCTTTRGCCAT 10345-10364 VP24 AUGGCUAAAGCUACGGGACG 12959-12978 35 20 82.94 16
EBOLAID055
Raw data
Min-max 		PCR primer forward ZEBOV-F TGGAAAAAACATTAAGAGAACACTTGC 847-873 NP UGGAAAAAACAUUAAGAGAACACUUGC 987-1013 3.7 0 77.88 17
EBOLAID056
Raw data
Min-max 		PCR primer reverse ZEBOV-R AGGAGAGAAACTGACCGGCAT 906-926 NP AUGCCGGUCAGUUUCUCUCCU 1046-1066 19.05 0 72.99 17
EBOLAID057
Raw data
Min-max 		Probe (FAM & BlackHole Quenche(...) ZEBOV-P CATGCCGGAAGAGGAGACAACTGAAGC 877-903 NP CAUGCCGGAAGAGGAGACAACUGAAGC 1017-1043 29.63 100 87.07 17
EBOLAID058
Raw data
Min-max 		PCR primer forward rt_EBOV-f ATTTGAATGGGGTCCAATTGCC 13997-14018 L AUUUGAAUGGGGUCCAAUUGCC 16968-16989 45.45 40 75.56 22
EBOLAID059
Raw data
Min-max 		PCR primer reverse rt_EBOL-r AAGCAGTRCCTATACTAGCCA 14090-14110 L UGGCUAGUAUAGGCACUGCUU 17061-17081 47.62 40 76.51 22
EBOLAID060
Raw data
Min-max 		Probe (Taqman) EBOV_prb AGTCCCTTAAAACGGCTACAAGAATGGGAC 14021-14050 L AGUCCCUUAAAACGGCUACAAGAAUGGCAC 16992-17018 37.04 20 78.31 22
EBOLAID061
Raw data
Min-max 		Primer forward F3 GACGGGAGTGAGTGTCTACC 6387-6406 GP GACGGGAGUGAGUGUCUACC 7822-7841 15 0 79.31 23
EBOLAID062
Raw data
Min-max 		Primer reverse B3 AGCTTGGGGCAGTATCAGAA 6586-6605 GP UUCUGAUACUGCCCCAAGCU 8021-8040 15 0 64.08 23
EBOLAID063
Raw data
Min-max 		Primer reverse FL GCACATACCGGCACC 6439-6453 GP GGUGCCGGUAUGUGC 7874-7888 13.33 20 76.05 23
EBOLAID064
Raw data
Min-max 		Primer forward BL CTTCCTGTATGATCGACTTGCTTC 6515-6538 GP CUUCCUGUAUGAUCGACUUGCUUC 7950-7973 29.17 60 73.42 23
EBOLAID065
Raw data
Min-max 		Primer forward F3 CAATAAACAACTATTTAAATAAC 18321-18343 3'UTR CAAUAAACAACUAUUUAAAUAAC 21904-21925 4.55 0 68.85 24
EBOLAID066
Raw data
Min-max 		Primer reverse B3 CTGGCAAGATATTGATACAACA 18530-18551 3'UTR UGUUGUAUCAAUAUCCUGUCAG 22145-22159 0 0 62.18 24
EBOLAID067
Raw data
Min-max 		Primer reverse LF AATTTTTTGATTATCACGC 18388-18406 3'UTR GCGUGAUAAUCAAAAAAUU 21981-22001 0 0 62.33 24
EBOLAID068
Raw data
Min-max 		Primer forward F3 TGAAGTCAAGAAGCGTGATGG 787-807 NP UGAAGUCAAGAAGCGUGAUGG 907-927 19.05 20 69.18 24
EBOLAID069
Raw data
Min-max 		Primer reverse B3 AGTCCTTGCTCTGCATGTACT 1000-1020 NP AGUACAUGCAGAGCAAGGACU 1140-1160 42.86 40 79.73 24
EBOLAID070
Raw data
Min-max 		Primer reverse LF TGTTTTTTCCACTAGATACTGCTGG 833-857 NP CCAGCAGUAUCUAGUGGAAAAAACA 973-997 8 20 74.82 24
EBOLAID071
Raw data
Min-max 		Primer forward LB TCCTTCCGAAATTGGTAGTAGGA 939-961 NP UCCUUCCGAAAUUGGUAGUAGGA 1079-1101 39.13 40 74.08 24
EBOLAID072
Raw data
Min-max 		Primer forward EBOV-F3 TGGTTCAAGTGCACAGTCAA 7086-7105 GP UGGUUCAAGUGCACAGUCAA 8577-8596 10 0 69.98 25
EBOLAID073
Raw data
Min-max 		Primer reverse EBOV-B3 TGTCTGCTCTACGGTGATGT 7255-7274 GP ACAUCACCGCAGAACAGACA 21399-21407 22.22 0 69.55 25
EBOLAID074
Raw data
Min-max 		Primer reverse EBOV-LF GCAAGGGTTGTCAGATGCG 7125-7143 GP CGCAUCUAACAACCCUUGC 8645-8655 0 0 61.52 25
EBOLAID075
Raw data
Min-max 		Primer forward EBOV-LB ATAATACACCCGTGTATAAACTTGAC 7203-7228 GP AUAAUACACCCGUGUAUAAACUUGAC 8732-8758 3.7 0 69.07 25
EBOLAID076
Raw data
Min-max 		PCR primer forward ZEBOV Forward CGAACTTGACCATCTTGGACTTG 1552-1574 NP CGAACUUGACCAUCUUGGACUUG 1692-1714 21.74 20 71.49 26
EBOLAID077
Raw data
Min-max 		PCR primer reverse ZEBOV Reverse TCCTCGTCGTCCTCGTCTAGAT 1929-1950 NP AUCUAGACGAGGACGACGAGGA 2089-2110 27.27 0 77.68 26
EBOLAID078
Raw data
Min-max 		Primer forward EBO-RPA-F TAGTAGGAGAAAAGGCTTGCCTTGAGAAGG(...) 954-983 NP UAGUAGGAGAAAAGGCUUGCCUUGAGAAGG 1094-1123 43.33 60 77.6 27
EBOLAID079
Raw data
Min-max 		Primer reverse EBO-RPA-R TGTTCGCATCAAACGGAAAATCACCATCAT(...) 1057-1087 NP CAUGAUGGUGAUUUUCCGUUUGAUGCGAAC(...) 1197-1227 29.03 60 76.38 27
EBOLAID080
Raw data
Min-max 		Probe EBO-RPA-P TCAAGTACATGCAGAGCAAGGACTGATACA(...) 997-1028 NP UCAAGUACAUGCAGAGCAAGGACUGAUACA(...) 1137-1168 31.25 20 78.59 27