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_alig06
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	6602-6621	70	80	96.74	1
EBOLAID002 Raw data Min-max	PCR primer reverse	EBO-2	ACGACACCTTCAGCRAAAGT	6561-6580	GP	ACUUUCGCUGAAGGUGUCGU	7061-7080	55	60	95.52	1
EBOLAID003 Raw data Min-max	PCR primer forward	EBO-3	GTTTGTCGKGACAAACTGTC	6192-6211	GP	GUUUGUCGUGACAAACUGUC	6692-6711	50	60	93.74	1
EBOLAID004 Raw data Min-max	PCR primer reverse	EBO-4	TGGAARGCWAAGTCWCCGG	6481-6499	GP	CCGGAGACUUUGCCUUCCA	6981-6999	47.37	40	95.33	1
EBOLAID005 Raw data Min-max	PCR primer forward	GAB-1	GAATGTAGGTAGAACCTTCGG	13251-13271	L	GAAUGUAGGUAGAACCUUCGG	14291-14311	52.38	80	95.19	1
EBOLAID006 Raw data Min-max	PCR primer reverse	GAB-2	GCATATAACACTGTGGGATTG	13583-13603	L	CAAUCCCACAGUGUUAUAUGC	14623-14643	66.67	40	96.66	1
EBOLAID007 Raw data Min-max	PCR primer forward	EBO-BP1	AATGGGCTGAAAATTGCTACAATC	6346-6369	GP	AAUGGGCUGAAAACUGCUACAAUC	6846-6869	75	60	98.83	2
EBOLAID008 Raw data Min-max	PCR primer reverse	EBO-GP2	TTTTTTTAGTTTCCCAGAAGGCCCACT	6898-6924	GP	AGUGGGCCUUCUGGGAAACUAAAAAAA	7398-7424	81.48	80	98.19	2
EBOLAID009 Raw data Min-max	PCR primer forward	ZAI-NP1	GGACCGCCAAGGTAAAAAATGA	1275-1296	NP	GGACCGCCAAGGUAAAAAAUGA	1376-1397	68.18	80	96.46	2
EBOLAID010 Raw data Min-max	PCR primer reverse	ZAI-NP2	GCATATTGTTGGAGTTGCTTCTCAGC	1517-1542	NP	GCUGAGAAGCAACUCCAACAAUAUGC	1618-1643	65.38	80	97.07	2
EBOLAID011 Raw data Min-max	PCR primer forward		ATCGGAATTTTCTTTCTCATTGAAAGA	13214-13241	L	AUCGGAACUUUUCUUUCUCAUUGAAAGA	14254-14281	71.43	80	97.27	3;4
EBOLAID012 Raw data Min-max	PCR primer reverse		ATGTGGTGGATTATAATAATCACTGACATG(...)	13600-13632	L	AUGCAUGUCAGUGAUUAUUAUAAUCCACCA(...)	14640-14672	81.82	80	97.78	3;4
EBOLAID013 Raw data Min-max	PCR primer forward	EBOGP-1Df	TGGGCTGAAAAYTGCTACAATC	6348-6369	GP	UGGGCUGAAAACUGCUACAAUC	6848-6869	77.27	60	99.01	5
EBOLAID014 Raw data Min-max	PCR primer reverse	EBOGP-1Dr	CTTTGTGMACATASCGGCAC	6440-6459	GP	GUGCCGGUAUGUGCACAAAG	6940-6959	80	80	98.17	5
EBOLAID015 Raw data Min-max	Probe	EBOGP-1DZPrb	CTACCAGCAGCGCCAGACGG	6402-6421	GP	CUACCAGCAGCGCCAGACGG	6902-6921	60	80	96	5
EBOLAID016 Raw data Min-max	PCR primer forward	FILO-A	ATCGGAATTTTTCTTTCTCATT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	14254-14275	72.73	80	97.53	2;1;5;6
EBOLAID017 Raw data Min-max	PCR primer reverse	FILO-B	ATGTGGTGGGTTATAATAATCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	14643-14672	83.33	80	97.82	2;1;5;6;7
EBOLAID018 Raw data Min-max	PCR primer forward	EBOORF UP	ATGGATTCTCGTCCTCAGAAAAT	470-492	NP	AUGGAUUCUCGUCCUCAGAAAAU	571-593	26.09	0	91.79	8
EBOLAID019 Raw data Min-max	PCR primer reverse	EBOORF DP	TCACTGATGATGTTGCAGGATT	2668-2689	NP	AAUCCUGCAACAUCAUCAGUGA	2814-2835	40.91	40	94.54	8
EBOLAID020 Raw data Min-max	PCR primer forward	ENZ FP	ATGATGGAAGCTACGGCG	1854-1871	NP	AUGAUGGAAGCUACGGCG	1955-1972	27.78	0	90.72	8
EBOLAID021 Raw data Min-max	PCR primer reverse	ENZ RP	AGGACCAAGTCATCTGGTGC	1904-1923	NP	GCACCAGAUGACUUGGUCCU	2005-2024	40	40	93.71	8
EBOLAID022 Raw data Min-max	Probe	ENZ P	CCAGAGTTACTCGGAAAACGGCATG	1876-1900	NP	CCAGAGUUACUCGGAAAACGGCAUG	1977-2001	8	0	88.15	8
EBOLAID023 Raw data Min-max	PCR primer forward	SudZaiNP1(+)	GAGACAACGGAAGCTAATGC	890-909	NP	GAGACAACUGAAGCUAAUGC	991-1010	80	100	96.93	9
EBOLAID024 Raw data Min-max	PCR primer reverse	SudZaiNP1(-)	AACGGAAGATCACCATCATG	1057-1076	NP	CAUGAUGGUGAUUUUCCGUU	1158-1177	70	80	97.34	9
EBOLAID025 Raw data Min-max	PCR primer forward	SudZaiNP2(+)	GGTCAGTTTCTATCCTTTGC	911-930	NP	GGUCAGUUUCUCUCCUUUGC	1012-1031	70	100	95.84	9
EBOLAID026 Raw data Min-max	PCR primer reverse	SudZaiNP2(-)	CATGTGTCCAACTGATTGCC	1041-1060	NP	GGCAAUCAGUAGGACACAUG	1142-1161	80	80	98.49	9
EBOLAID027 Raw data Min-max	PCR primer forward	EBsp5	TTYCCTAGCAAYATGATGG	13345-13363	L	UUUCCUAGCAAUAUGAUGG	14385-14403	78.95	100	98.49	10;4
EBOLAID028 Raw data Min-max	PCR primer reverse	EBsp3	TATAATAATCACTGACATGCAT	13600-13621	L	AUGCAUGUCAGUGAUUAUUAUA	14640-14661	86.36	80	98.79	10;4
EBOLAID029 Raw data Min-max	PCR primer forward	evR3	TCTTGCAAGGACCGCCAAGGTAAAAA	1267-1292	NP	UCUUGCAAGGACCGCCAAGGUAAAAA	1368-1393	57.69	60	94.84	11
EBOLAID030 Raw data Min-max	PCR primer reverse	evF3	TTCAAAAGTCGGGCGAAAGGAGCATA	1346-1371	NP	UAUGCUCCUUUCGCCCGACUUUUGAA	1447-1472	65.38	100	95.96	11
EBOLAID031 Raw data Min-max	PCR primer forward	F3	AATAACGAAAGGAGTCCCTA	18338-18357	3'UTR	AAUAACGAAAGGAGUCCCUA	19600-19616	5.88	0	88.07	12
EBOLAID032 Raw data Min-max	PCR primer reverse	B3	TTGTATCAATATCCTGTCAG	18532-18551	3'UTR	UUGUAUCAAUAUCCUGUCAG	19834-19853	5	20	88.79	12
EBOLAID033 Raw data Min-max	PCR primer forward	Ebola-1F	GATGCAGTATTCGAGCCTAATGTTCTAG	13063-13090	L	GAUGCAGUAUUCGAGCCUAAUGUUCUAG	14103-14130	71.43	60	97.22	13
EBOLAID034 Raw data Min-max	PCR primer reverse	Ebola-1R	GTGTTTGAACATTGCGAGTCGGATAAG	13280-13306	L	CUUAUCCGACUCGCAAUGUUCAAACAC	14320-14346	59.26	60	96.22	13
EBOLAID035 Raw data Min-max	Probe	Ebola-P	ACTCGAGTATCTACTACCACAATATCGGAA(...)	13191-13221	L	ACUCGAGUAUCUACUACCACAAUAUCGGAA(...)	14231-14261	45.16	60	94.9	13
EBOLAID036 Raw data Min-max	PCR primer forward	FiloA2.4	AAGCATTTCCTAGCAATATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	14380-14404	80	100	98.3	7
EBOLAID037 Raw data Min-max	PCR primer forward	FiloA2.2	AAGCCTTTCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	14380-14404	80	100	98.3	7
EBOLAID038 Raw data Min-max	PCR primer forward	FiloA2.3	AAGCATTCCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	14380-14404	80	100	98.3	7
EBOLAID039 Raw data Min-max	PCR primer reverse	FILO B-Ra	GTGAGGAGGGCTATAAAAGTCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	14643-14661	89.47	80	99.02	7
EBOLAID040 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOSu	CCGAAATCATCACTIGTITGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	14451-14473	73.91	80	98.32	7
EBOLAID041 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOg	CCAAAATCATCACTIGTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	14451-14476	73.08	80	97.61	7
EBOLAID042 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMMBG	CCTATGCTTGCTGAATTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	14451-14460	70	40	98.19	7
EBOLAID043 Raw data Min-max	PCR primer forward	F565	TCTGACATGGATTACCACAAGATC	518-541	NP	UCUGACAUGGAUUACCACAAGAUC	619-642	54.17	60	94.63	14
EBOLAID044 Raw data Min-max	PCR primer reverse	R640	GGATGACTCTTTGCCGAACAATC	571-593	NP	GAUUGUUCGGCAAAGAGUCAUCC	672-694	52.17	60	97.01	14
EBOLAID045 Raw data Min-max	Probe (FAM&MGB)	p597S	AGGTCTGTCCGTTCAA	550-565	NP	AGGUCUGUCCGUUCAA	651-666	56.25	60	95.17	14
EBOLAID046 Raw data Min-max	PCR primer forward	F2000	TTTTCAATCCTCAACCGTAAGGC	7781-7803	GP	UUUUCAAUCCUCAACCGUAAGGC	8339-8361	52.17	80	95.05	14
EBOLAID047 Raw data Min-max	PCR primer reverse	R2079	CAGTCCGGTCCCAGAATGTG	7841-7860	GP	CACAUUCUGGGACCGGACUG	8399-8418	55	40	94.71	14
EBOLAID048 Raw data Min-max	Probe (FAM&TAMRA)	p2058A	CATGTGCCGCCCCATCGCTGC	7819-7839	GP	GCAGCGAUGGGGCGGCACAUG	8377-8397	57.14	80	95.14	14
EBOLAID049 Raw data Min-max	PCR primer forward	PanFilo-L1	ATMGRAAYTTTTCYTTYTCWYT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	14254-14272	73.68	80	97.56	15
EBOLAID050 Raw data Min-max	PCR primer reverse	Pan?lo-L2	TGWGGHGGRYTATAAWARTCACTDACAT	13604-13631	L	AUGUCAGUGAUUAUUAUAAUCCACCACA	14644-14671	82.14	60	97.67	15
EBOLAID051 Raw data Min-max	PCR primer forward	PanFilo-L3	GCNAARGCMTTYCCHAGYAAYATGATGG	13336-13363	L	GCUAAAGCAUUUCCUAGCAAUAUGAUGG	14379-14403	80	100	98.3	15
EBOLAID052 Raw data Min-max	PCR primer reverse	Pan?lo-L4	ATAAWARTCACTDACATGCATRTARCA	13594-13620	L	UGUUAUAUGCAUGUCAGUGAUUAUUAU	14634-14660	85.19	100	98.71	15
EBOLAID053 Raw data Min-max	PCR primer forward	KGH-F	GTCGTTCCAACAATCGAGCG	10243-10262	VP24	GUCGUUCCAACAAUCGAGCG	11146-11165	10	20	91.17	16
EBOLAID054 Raw data Min-max	PCR primer forward	KGH-R	CGTCCCGTAGCTTTRGCCAT	10345-10364	VP24	AUGGCUAAAGCUACGGGACG	11248-11267	70	60	95.31	16
EBOLAID055 Raw data Min-max	PCR primer forward	ZEBOV-F	TGGAAAAAACATTAAGAGAACACTTGC	847-873	NP	UGGAAAAAACAUUAAGAGAACACUUGC	948-974	62.96	60	94.75	17
EBOLAID056 Raw data Min-max	PCR primer reverse	ZEBOV-R	AGGAGAGAAACTGACCGGCAT	906-926	NP	AUGCCGGUCAGUUUCUCUCCU	1007-1027	66.67	80	95.38	17
EBOLAID057 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	ZEBOV-P	CATGCCGGAAGAGGAGACAACTGAAGC	877-903	NP	CAUGCCGGAAGAGGAGACAACUGAAGC	978-1004	77.78	100	96.76	17
EBOLAID058 Raw data Min-max	PCR primer forward	rt_EBOV-f	ATTTGAATGGGGTCCAATTGCC	13997-14018	L	AUUUGAAUGGGGUCCAAUUGCC	15037-15058	68.18	80	96.78	22
EBOLAID059 Raw data Min-max	PCR primer reverse	rt_EBOL-r	AAGCAGTRCCTATACTAGCCA	14090-14110	L	UGGCUAGUAUAGGCACUGCUU	15130-15150	71.43	60	95.77	22
EBOLAID060 Raw data Min-max	Probe (Taqman)	EBOV_prb	AGTCCCTTAAAACGGCTACAAGAATGGGAC	14021-14050	L	AGUCCCUUAAAACGGCUACAAGAAUGGCAC	15061-15087	62.96	60	95.19	22
EBOLAID061 Raw data Min-max	Primer forward	F3	GACGGGAGTGAGTGTCTACC	6387-6406	GP	GACGGGAGUGAGUGUCUACC	6887-6906	70	80	96.64	23
EBOLAID062 Raw data Min-max	Primer reverse	B3	AGCTTGGGGCAGTATCAGAA	6586-6605	GP	UUCUGAUACUGCCCCAAGCU	7086-7105	45	60	94.22	23
EBOLAID063 Raw data Min-max	Primer reverse	FL	GCACATACCGGCACC	6439-6453	GP	GGUGCCGGUAUGUGC	6939-6953	80	80	97.98	23
EBOLAID064 Raw data Min-max	Primer forward	BL	CTTCCTGTATGATCGACTTGCTTC	6515-6538	GP	CUUCCUGUAUGAUCGACUUGCUUC	7015-7038	70.83	80	97.31	23
EBOLAID065 Raw data Min-max	Primer forward	F3	CAATAAACAACTATTTAAATAAC	18321-18343	3'UTR	CAAUAAACAACUAUUUAAAUAAC	19561-19573	15.38	20	88.73	24
EBOLAID066 Raw data Min-max	Primer reverse	B3	CTGGCAAGATATTGATACAACA	18530-18551	3'UTR	UGUUGUAUCAAUAUCCUGUCAG	19832-19846	6.67	0	91.53	24
EBOLAID067 Raw data Min-max	Primer reverse	LF	AATTTTTTGATTATCACGC	18388-18406	3'UTR	GCGUGAUAAUCAAAAAAUU	19647-19665	10.53	80	94	24
EBOLAID068 Raw data Min-max	Primer forward	F3	TGAAGTCAAGAAGCGTGATGG	787-807	NP	UGAAGUCAAGAAGCGUGAUGG	888-908	33.33	40	91.2	24
EBOLAID069 Raw data Min-max	Primer reverse	B3	AGTCCTTGCTCTGCATGTACT	1000-1020	NP	AGUACAUGCAGAGCAAGGACU	1101-1121	57.14	60	96.88	24
EBOLAID070 Raw data Min-max	Primer reverse	LF	TGTTTTTTCCACTAGATACTGCTGG	833-857	NP	CCAGCAGUAUCUAGUGGAAAAAACA	934-958	40	40	92.2	24
EBOLAID071 Raw data Min-max	Primer forward	LB	TCCTTCCGAAATTGGTAGTAGGA	939-961	NP	UCCUUCCGAAAUUGGUAGUAGGA	1040-1062	60.87	60	95.37	24
EBOLAID072 Raw data Min-max	Primer forward	EBOV-F3	TGGTTCAAGTGCACAGTCAA	7086-7105	GP	UGGUUCAAGUGCACAGUCAA	7586-7605	40	0	94.81	25
EBOLAID073 Raw data Min-max	Primer reverse	EBOV-B3	TGTCTGCTCTACGGTGATGT	7255-7274	GP	ACAUCACCGCAGAACAGACA	7755-7774	20	40	90.14	25
EBOLAID074 Raw data Min-max	Primer reverse	EBOV-LF	GCAAGGGTTGTCAGATGCG	7125-7143	GP	CGCAUCUAACAACCCUUGC	7625-7643	10.53	20	92.15	25
EBOLAID075 Raw data Min-max	Primer forward	EBOV-LB	ATAATACACCCGTGTATAAACTTGAC	7203-7228	GP	AUAAUACACCCGUGUAUAAACUUGAC	7703-7728	7.69	0	92.33	25
EBOLAID076 Raw data Min-max	PCR primer forward	ZEBOV Forward	CGAACTTGACCATCTTGGACTTG	1552-1574	NP	CGAACUUGACCAUCUUGGACUUG	1653-1675	56.52	60	95.44	26
EBOLAID077 Raw data Min-max	PCR primer reverse	ZEBOV Reverse	TCCTCGTCGTCCTCGTCTAGAT	1929-1950	NP	AUCUAGACGAGGACGACGAGGA	2030-2051	54.55	40	95.06	26
EBOLAID078 Raw data Min-max	Primer forward	EBO-RPA-F	TAGTAGGAGAAAAGGCTTGCCTTGAGAAGG(...)	954-983	NP	UAGUAGGAGAAAAGGCUUGCCUUGAGAAGG	1055-1084	66.67	60	95.83	27
EBOLAID079 Raw data Min-max	Primer reverse	EBO-RPA-R	TGTTCGCATCAAACGGAAAATCACCATCAT(...)	1057-1087	NP	CAUGAUGGUGAUUUUCCGUUUGAUGCGAAC(...)	1158-1188	67.74	80	97.5	27
EBOLAID080 Raw data Min-max	Probe	EBO-RPA-P	TCAAGTACATGCAGAGCAAGGACTGATACA(...)	997-1028	NP	UCAAGUACAUGCAGAGCAAGGACUGAUACA(...)	1098-1129	62.5	80	96.96	27