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_alig07
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	6112-6131	35	40	99.92	1
EBOLAID002 Raw data Min-max	PCR primer reverse	EBO-2	ACGACACCTTCAGCRAAAGT	6561-6580	GP	ACUUUCGCUGAAGGUGUCGU	6571-6590	30	20	99.97	1
EBOLAID003 Raw data Min-max	PCR primer forward	EBO-3	GTTTGTCGKGACAAACTGTC	6192-6211	GP	GUUUGUCGUGACAAACUGUC	6202-6221	20	40	99.96	1
EBOLAID004 Raw data Min-max	PCR primer reverse	EBO-4	TGGAARGCWAAGTCWCCGG	6481-6499	GP	CCGGAGACUUUGCCUUCCA	6491-6509	5.26	100	99.97	1
EBOLAID005 Raw data Min-max	PCR primer forward	GAB-1	GAATGTAGGTAGAACCTTCGG	13251-13271	L	GAAUGUAGGUAGAACCUUCGG	13277-13297	71.43	100	99.98	1
EBOLAID006 Raw data Min-max	PCR primer reverse	GAB-2	GCATATAACACTGTGGGATTG	13583-13603	L	CAAUCCCACAGUGUUAUAUGC	13609-13629	38.1	100	99.99	1
EBOLAID007 Raw data Min-max	PCR primer forward	EBO-BP1	AATGGGCTGAAAATTGCTACAATC	6346-6369	GP	AAUGGGCUGAAAACUGCUACAAUC	6356-6379	16.67	0	99.67	2
EBOLAID008 Raw data Min-max	PCR primer reverse	EBO-GP2	TTTTTTTAGTTTCCCAGAAGGCCCACT	6898-6924	GP	AGUGGGCCUUCUGGGAAACUAAAAAAA	6908-6934	0	0	99.97	2
EBOLAID009 Raw data Min-max	PCR primer forward	ZAI-NP1	GGACCGCCAAGGTAAAAAATGA	1275-1296	NP	GGACCGCCAAGGUAAAAAAUGA	1278-1299	59.09	60	99.99	2
EBOLAID010 Raw data Min-max	PCR primer reverse	ZAI-NP2	GCATATTGTTGGAGTTGCTTCTCAGC	1517-1542	NP	GCUGAGAAGCAACUCCAACAAUAUGC	1521-1546	34.62	0	99.97	2
EBOLAID011 Raw data Min-max	PCR primer forward		ATCGGAATTTTCTTTCTCATTGAAAGA	13214-13241	L	AUCGGAACUUUUCUUUCUCAUUGAAAGA	13239-13267	51.72	20	99.99	3;4
EBOLAID012 Raw data Min-max	PCR primer reverse		ATGTGGTGGATTATAATAATCACTGACATG(...)	13600-13632	L	AUGCAUGUCAGUGAUUAUUAUAAUCCACCA(...)	13626-13658	6.06	100	99.84	3;4
EBOLAID013 Raw data Min-max	PCR primer forward	EBOGP-1Df	TGGGCTGAAAAYTGCTACAATC	6348-6369	GP	UGGGCUGAAAACUGCUACAAUC	6358-6379	13.64	0	99.64	5
EBOLAID014 Raw data Min-max	PCR primer reverse	EBOGP-1Dr	CTTTGTGMACATASCGGCAC	6440-6459	GP	GUGCCGGUAUGUGCACAAAG	6450-6469	0	0	99.99	5
EBOLAID015 Raw data Min-max	Probe	EBOGP-1DZPrb	CTACCAGCAGCGCCAGACGG	6402-6421	GP	CUACCAGCAGCGCCAGACGG	6412-6431	0	20	99.99	5
EBOLAID016 Raw data Min-max	PCR primer forward	FILO-A	ATCGGAATTTTTCTTTCTCATT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	13239-13261	56.52	100	99.99	2;1;5;6
EBOLAID017 Raw data Min-max	PCR primer reverse	FILO-B	ATGTGGTGGGTTATAATAATCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	13629-13658	6.67	80	99.82	2;1;5;6;7
EBOLAID018 Raw data Min-max	PCR primer forward	EBOORF UP	ATGGATTCTCGTCCTCAGAAAAT	470-492	NP	AUGGAUUCUCGUCCUCAGAAAAU	473-495	26.09	20	99.87	8
EBOLAID019 Raw data Min-max	PCR primer reverse	EBOORF DP	TCACTGATGATGTTGCAGGATT	2668-2689	NP	AAUCCUGCAACAUCAUCAGUGA	2672-2693	77.27	100	99.98	8
EBOLAID020 Raw data Min-max	PCR primer forward	ENZ FP	ATGATGGAAGCTACGGCG	1854-1871	NP	AUGAUGGAAGCUACGGCG	1858-1875	33.33	40	99.97	8
EBOLAID021 Raw data Min-max	PCR primer reverse	ENZ RP	AGGACCAAGTCATCTGGTGC	1904-1923	NP	GCACCAGAUGACUUGGUCCU	1908-1927	80	100	99.98	8
EBOLAID022 Raw data Min-max	Probe	ENZ P	CCAGAGTTACTCGGAAAACGGCATG	1876-1900	NP	CCAGAGUUACUCGGAAAACGGCAUG	1880-1904	24	100	99.99	8
EBOLAID023 Raw data Min-max	PCR primer forward	SudZaiNP1(+)	GAGACAACGGAAGCTAATGC	890-909	NP	GAGACAACUGAAGCUAAUGC	893-912	5	40	99.83	9
EBOLAID024 Raw data Min-max	PCR primer reverse	SudZaiNP1(-)	AACGGAAGATCACCATCATG	1057-1076	NP	CAUGAUGGUGAUUUUCCGUU	1060-1079	60	100	99.99	9
EBOLAID025 Raw data Min-max	PCR primer forward	SudZaiNP2(+)	GGTCAGTTTCTATCCTTTGC	911-930	NP	GGUCAGUUUCUCUCCUUUGC	914-933	0	80	99.99	9
EBOLAID026 Raw data Min-max	PCR primer reverse	SudZaiNP2(-)	CATGTGTCCAACTGATTGCC	1041-1060	NP	GGCAAUCAGUAGGACACAUG	1044-1063	75	60	99.98	9
EBOLAID027 Raw data Min-max	PCR primer forward	EBsp5	TTYCCTAGCAAYATGATGG	13345-13363	L	UUUCCUAGCAAUAUGAUGG	13371-13389	15.79	100	99.77	10;4
EBOLAID028 Raw data Min-max	PCR primer reverse	EBsp3	TATAATAATCACTGACATGCAT	13600-13621	L	AUGCAUGUCAGUGAUUAUUAUA	13626-13647	63.64	100	99.78	10;4
EBOLAID029 Raw data Min-max	PCR primer forward	evR3	TCTTGCAAGGACCGCCAAGGTAAAAA	1267-1292	NP	UCUUGCAAGGACCGCCAAGGUAAAAA	1270-1295	50	20	99.99	11
EBOLAID030 Raw data Min-max	PCR primer reverse	evF3	TTCAAAAGTCGGGCGAAAGGAGCATA	1346-1371	NP	UAUGCUCCUUUCGCCCGACUUUUGAA	1349-1374	0	20	100	11
EBOLAID031 Raw data Min-max	PCR primer forward	F3	AATAACGAAAGGAGTCCCTA	18338-18357	3'UTR	AAUAACGAAAGGAGUCCCUA	18365-18384	0	0	99.34	12
EBOLAID032 Raw data Min-max	PCR primer reverse	B3	TTGTATCAATATCCTGTCAG	18532-18551	3'UTR	UUGUAUCAAUAUCCUGUCAG	18560-18579	0	20	99.85	12
EBOLAID033 Raw data Min-max	PCR primer forward	Ebola-1F	GATGCAGTATTCGAGCCTAATGTTCTAG	13063-13090	L	GAUGCAGUAUUCGAGCCUAAUGUUCUAG	13088-13115	78.57	60	99.99	13
EBOLAID034 Raw data Min-max	PCR primer reverse	Ebola-1R	GTGTTTGAACATTGCGAGTCGGATAAG	13280-13306	L	CUUAUCCGACUCGCAAUGUUCAAACAC	13306-13332	0	40	99.94	13
EBOLAID035 Raw data Min-max	Probe	Ebola-P	ACTCGAGTATCTACTACCACAATATCGGAA(...)	13191-13221	L	ACUCGAGUAUCUACUACCACAAUAUCGGAA(...)	13216-13246	12.9	0	99.96	13
EBOLAID036 Raw data Min-max	PCR primer forward	FiloA2.4	AAGCATTTCCTAGCAATATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13366-13390	32	100	99.83	7
EBOLAID037 Raw data Min-max	PCR primer forward	FiloA2.2	AAGCCTTTCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13366-13390	32	100	99.83	7
EBOLAID038 Raw data Min-max	PCR primer forward	FiloA2.3	AAGCATTCCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13366-13390	32	100	99.83	7
EBOLAID039 Raw data Min-max	PCR primer reverse	FILO B-Ra	GTGAGGAGGGCTATAAAAGTCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	13629-13647	57.89	80	99.75	7
EBOLAID040 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOSu	CCGAAATCATCACTIGTITGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13437-13459	60.87	40	99.88	7
EBOLAID041 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOg	CCAAAATCATCACTIGTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13437-13462	53.85	20	99.87	7
EBOLAID042 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMMBG	CCTATGCTTGCTGAATTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13437-13446	80	60	100	7
EBOLAID043 Raw data Min-max	PCR primer forward	F565	TCTGACATGGATTACCACAAGATC	518-541	NP	UCUGACAUGGAUUACCACAAGAUC	521-544	0	100	99.98	14
EBOLAID044 Raw data Min-max	PCR primer reverse	R640	GGATGACTCTTTGCCGAACAATC	571-593	NP	GAUUGUUCGGCAAAGAGUCAUCC	574-596	43.48	20	99.98	14
EBOLAID045 Raw data Min-max	Probe (FAM&MGB)	p597S	AGGTCTGTCCGTTCAA	550-565	NP	AGGUCUGUCCGUUCAA	553-568	37.5	60	99.99	14
EBOLAID046 Raw data Min-max	PCR primer forward	F2000	TTTTCAATCCTCAACCGTAAGGC	7781-7803	GP	UUUUCAAUCCUCAACCGUAAGGC	7791-7813	52.17	60	100	14
EBOLAID047 Raw data Min-max	PCR primer reverse	R2079	CAGTCCGGTCCCAGAATGTG	7841-7860	GP	CACAUUCUGGGACCGGACUG	7851-7870	70	60	99.98	14
EBOLAID048 Raw data Min-max	Probe (FAM&TAMRA)	p2058A	CATGTGCCGCCCCATCGCTGC	7819-7839	GP	GCAGCGAUGGGGCGGCACAUG	7829-7849	14.29	20	99.99	14
EBOLAID049 Raw data Min-max	PCR primer forward	PanFilo-L1	ATMGRAAYTTTTCYTTYTCWYT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	13239-13261	56.52	100	99.99	15
EBOLAID050 Raw data Min-max	PCR primer reverse	Pan?lo-L2	TGWGGHGGRYTATAAWARTCACTDACAT	13604-13631	L	AUGUCAGUGAUUAUUAUAAUCCACCACA	13630-13657	7.14	60	99.82	15
EBOLAID051 Raw data Min-max	PCR primer forward	PanFilo-L3	GCNAARGCMTTYCCHAGYAAYATGATGG	13336-13363	L	GCUAAAGCAUUUCCUAGCAAUAUGAUGG	13365-13389	32	100	99.83	15
EBOLAID052 Raw data Min-max	PCR primer reverse	Pan?lo-L4	ATAAWARTCACTDACATGCATRTARCA	13594-13620	L	UGUUAUAUGCAUGUCAGUGAUUAUUAU	13620-13646	59.26	60	99.82	15
EBOLAID053 Raw data Min-max	PCR primer forward	KGH-F	GTCGTTCCAACAATCGAGCG	10243-10262	VP24	GUCGUUCCAACAAUCGAGCG	10263-10282	75	100	99.81	16
EBOLAID054 Raw data Min-max	PCR primer forward	KGH-R	CGTCCCGTAGCTTTRGCCAT	10345-10364	VP24	AUGGCUAAAGCUACGGGACG	10367-10386	90	100	99.99	16
EBOLAID055 Raw data Min-max	PCR primer forward	ZEBOV-F	TGGAAAAAACATTAAGAGAACACTTGC	847-873	NP	UGGAAAAAACAUUAAGAGAACACUUGC	850-876	11.11	40	99.98	17
EBOLAID056 Raw data Min-max	PCR primer reverse	ZEBOV-R	AGGAGAGAAACTGACCGGCAT	906-926	NP	AUGCCGGUCAGUUUCUCUCCU	909-929	0	60	99.97	17
EBOLAID057 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	ZEBOV-P	CATGCCGGAAGAGGAGACAACTGAAGC	877-903	NP	CAUGCCGGAAGAGGAGACAACUGAAGC	880-906	0	80	99.9	17
EBOLAID058 Raw data Min-max	PCR primer forward	rt_EBOV-f	ATTTGAATGGGGTCCAATTGCC	13997-14018	L	AUUUGAAUGGGGUCCAAUUGCC	14023-14044	0	20	99.98	22
EBOLAID059 Raw data Min-max	PCR primer reverse	rt_EBOL-r	AAGCAGTRCCTATACTAGCCA	14090-14110	L	UGGCUAGUAUAGGCACUGCUU	14116-14136	52.38	80	99.98	22
EBOLAID060 Raw data Min-max	Probe (Taqman)	EBOV_prb	AGTCCCTTAAAACGGCTACAAGAATGGGAC	14021-14050	L	AGUCCCUUAAAACGGCUACAAGAAUGGCAC	14047-14073	0	100	99.94	22
EBOLAID061 Raw data Min-max	Primer forward	F3	GACGGGAGTGAGTGTCTACC	6387-6406	GP	GACGGGAGUGAGUGUCUACC	6397-6416	55	40	99.99	23
EBOLAID062 Raw data Min-max	Primer reverse	B3	AGCTTGGGGCAGTATCAGAA	6586-6605	GP	UUCUGAUACUGCCCCAAGCU	6596-6615	30	40	99.99	23
EBOLAID063 Raw data Min-max	Primer reverse	FL	GCACATACCGGCACC	6439-6453	GP	GGUGCCGGUAUGUGC	6449-6463	0	0	99.98	23
EBOLAID064 Raw data Min-max	Primer forward	BL	CTTCCTGTATGATCGACTTGCTTC	6515-6538	GP	CUUCCUGUAUGAUCGACUUGCUUC	6525-6548	50	80	99.99	23
EBOLAID065 Raw data Min-max	Primer forward	F3	CAATAAACAACTATTTAAATAAC	18321-18343	3'UTR	CAAUAAACAACUAUUUAAAUAAC	18348-18370	0	0	99.93	24
EBOLAID066 Raw data Min-max	Primer reverse	B3	CTGGCAAGATATTGATACAACA	18530-18551	3'UTR	UGUUGUAUCAAUAUCCUGUCAG	18558-18572	0	0	99.99	24
EBOLAID067 Raw data Min-max	Primer reverse	LF	AATTTTTTGATTATCACGC	18388-18406	3'UTR	GCGUGAUAAUCAAAAAAUU	18415-18434	5	100	99.97	24
EBOLAID068 Raw data Min-max	Primer forward	F3	TGAAGTCAAGAAGCGTGATGG	787-807	NP	UGAAGUCAAGAAGCGUGAUGG	790-810	33.33	80	99.19	24
EBOLAID069 Raw data Min-max	Primer reverse	B3	AGTCCTTGCTCTGCATGTACT	1000-1020	NP	AGUACAUGCAGAGCAAGGACU	1003-1023	14.29	80	100	24
EBOLAID070 Raw data Min-max	Primer reverse	LF	TGTTTTTTCCACTAGATACTGCTGG	833-857	NP	CCAGCAGUAUCUAGUGGAAAAAACA	836-860	36	60	99.97	24
EBOLAID071 Raw data Min-max	Primer forward	LB	TCCTTCCGAAATTGGTAGTAGGA	939-961	NP	UCCUUCCGAAAUUGGUAGUAGGA	942-964	0	40	100	24
EBOLAID072 Raw data Min-max	Primer forward	EBOV-F3	TGGTTCAAGTGCACAGTCAA	7086-7105	GP	UGGUUCAAGUGCACAGUCAA	7096-7115	20	20	99.98	25
EBOLAID073 Raw data Min-max	Primer reverse	EBOV-B3	TGTCTGCTCTACGGTGATGT	7255-7274	GP	ACAUCACCGCAGAACAGACA	7265-7284	0	40	99.17	25
EBOLAID074 Raw data Min-max	Primer reverse	EBOV-LF	GCAAGGGTTGTCAGATGCG	7125-7143	GP	CGCAUCUAACAACCCUUGC	7135-7153	26.32	80	99.95	25
EBOLAID075 Raw data Min-max	Primer forward	EBOV-LB	ATAATACACCCGTGTATAAACTTGAC	7203-7228	GP	AUAAUACACCCGUGUAUAAACUUGAC	7213-7238	15.38	20	99.92	25
EBOLAID076 Raw data Min-max	PCR primer forward	ZEBOV Forward	CGAACTTGACCATCTTGGACTTG	1552-1574	NP	CGAACUUGACCAUCUUGGACUUG	1556-1578	60.87	100	99.98	26
EBOLAID077 Raw data Min-max	PCR primer reverse	ZEBOV Reverse	TCCTCGTCGTCCTCGTCTAGAT	1929-1950	NP	AUCUAGACGAGGACGACGAGGA	1933-1954	68.18	80	99.88	26
EBOLAID078 Raw data Min-max	Primer forward	EBO-RPA-F	TAGTAGGAGAAAAGGCTTGCCTTGAGAAGG(...)	954-983	NP	UAGUAGGAGAAAAGGCUUGCCUUGAGAAGG	957-986	10	100	100	27
EBOLAID079 Raw data Min-max	Primer reverse	EBO-RPA-R	TGTTCGCATCAAACGGAAAATCACCATCAT(...)	1057-1087	NP	CAUGAUGGUGAUUUUCCGUUUGAUGCGAAC(...)	1060-1090	64.52	100	99.99	27
EBOLAID080 Raw data Min-max	Probe	EBO-RPA-P	TCAAGTACATGCAGAGCAAGGACTGATACA(...)	997-1028	NP	UCAAGUACAUGCAGAGCAAGGACUGAUACA(...)	1000-1031	28.12	60	99.99	27