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_alig03
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	6297-6316	70	80	94.63	1
EBOLAID002 Raw data Min-max	PCR primer reverse	EBO-2	ACGACACCTTCAGCRAAAGT	6561-6580	GP	ACUUUCGCUGAAGGUGUCGU	6756-6775	55	60	92.64	1
EBOLAID003 Raw data Min-max	PCR primer forward	EBO-3	GTTTGTCGKGACAAACTGTC	6192-6211	GP	GUUUGUCGUGACAAACUGUC	6387-6406	50	60	89.82	1
EBOLAID004 Raw data Min-max	PCR primer reverse	EBO-4	TGGAARGCWAAGTCWCCGG	6481-6499	GP	CCGGAGACUUUGCCUUCCA	6676-6694	47.37	40	91.81	1
EBOLAID005 Raw data Min-max	PCR primer forward	GAB-1	GAATGTAGGTAGAACCTTCGG	13251-13271	L	GAAUGUAGGUAGAACCUUCGG	13775-13795	52.38	80	90.41	1
EBOLAID006 Raw data Min-max	PCR primer reverse	GAB-2	GCATATAACACTGTGGGATTG	13583-13603	L	CAAUCCCACAGUGUUAUAUGC	14107-14127	66.67	40	93.69	1
EBOLAID007 Raw data Min-max	PCR primer forward	EBO-BP1	AATGGGCTGAAAATTGCTACAATC	6346-6369	GP	AAUGGGCUGAAAACUGCUACAAUC	6541-6564	70.83	60	97.65	2
EBOLAID008 Raw data Min-max	PCR primer reverse	EBO-GP2	TTTTTTTAGTTTCCCAGAAGGCCCACT	6898-6924	GP	AGUGGGCCUUCUGGGAAACUAAAAAAA	7093-7119	81.48	80	97.1	2
EBOLAID009 Raw data Min-max	PCR primer forward	ZAI-NP1	GGACCGCCAAGGTAAAAAATGA	1275-1296	NP	GGACCGCCAAGGUAAAAAAUGA	1307-1328	59.09	80	91.83	2
EBOLAID010 Raw data Min-max	PCR primer reverse	ZAI-NP2	GCATATTGTTGGAGTTGCTTCTCAGC	1517-1542	NP	GCUGAGAAGCAACUCCAACAAUAUGC	1549-1574	65.38	80	96.51	2
EBOLAID011 Raw data Min-max	PCR primer forward		ATCGGAATTTTCTTTCTCATTGAAAGA	13214-13241	L	AUCGGAACUUUUCUUUCUCAUUGAAAGA	13738-13765	60.71	80	94.46	3;4
EBOLAID012 Raw data Min-max	PCR primer reverse		ATGTGGTGGATTATAATAATCACTGACATG(...)	13600-13632	L	AUGCAUGUCAGUGAUUAUUAUAAUCCACCA(...)	14124-14156	81.82	80	96.04	3;4
EBOLAID013 Raw data Min-max	PCR primer forward	EBOGP-1Df	TGGGCTGAAAAYTGCTACAATC	6348-6369	GP	UGGGCUGAAAACUGCUACAAUC	6543-6564	72.73	60	97.79	5
EBOLAID014 Raw data Min-max	PCR primer reverse	EBOGP-1Dr	CTTTGTGMACATASCGGCAC	6440-6459	GP	GUGCCGGUAUGUGCACAAAG	6635-6654	75	60	95.47	5
EBOLAID015 Raw data Min-max	Probe	EBOGP-1DZPrb	CTACCAGCAGCGCCAGACGG	6402-6421	GP	CUACCAGCAGCGCCAGACGG	6597-6616	50	80	90.01	5
EBOLAID016 Raw data Min-max	PCR primer forward	FILO-A	ATCGGAATTTTTCTTTCTCATT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	13738-13759	59.09	60	94.69	2;1;5;6
EBOLAID017 Raw data Min-max	PCR primer reverse	FILO-B	ATGTGGTGGGTTATAATAATCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	14127-14156	83.33	100	95.95	2;1;5;6;7
EBOLAID018 Raw data Min-max	PCR primer forward	EBOORF UP	ATGGATTCTCGTCCTCAGAAAAT	470-492	NP	AUGGAUUCUCGUCCUCAGAAAAU	502-524	26.09	0	82.94	8
EBOLAID019 Raw data Min-max	PCR primer reverse	EBOORF DP	TCACTGATGATGTTGCAGGATT	2668-2689	NP	AAUCCUGCAACAUCAUCAGUGA	2710-2731	36.36	20	89.51	8
EBOLAID020 Raw data Min-max	PCR primer forward	ENZ FP	ATGATGGAAGCTACGGCG	1854-1871	NP	AUGAUGGAAGCUACGGCG	1886-1903	27.78	0	81.63	8
EBOLAID021 Raw data Min-max	PCR primer reverse	ENZ RP	AGGACCAAGTCATCTGGTGC	1904-1923	NP	GCACCAGAUGACUUGGUCCU	1936-1955	35	40	88.14	8
EBOLAID022 Raw data Min-max	Probe	ENZ P	CCAGAGTTACTCGGAAAACGGCATG	1876-1900	NP	CCAGAGUUACUCGGAAAACGGCAUG	1908-1932	8	0	77.41	8
EBOLAID023 Raw data Min-max	PCR primer forward	SudZaiNP1(+)	GAGACAACGGAAGCTAATGC	890-909	NP	GAGACAACUGAAGCUAAUGC	922-941	80	100	94.87	9
EBOLAID024 Raw data Min-max	PCR primer reverse	SudZaiNP1(-)	AACGGAAGATCACCATCATG	1057-1076	NP	CAUGAUGGUGAUUUUCCGUU	1089-1108	65	80	94.58	9
EBOLAID025 Raw data Min-max	PCR primer forward	SudZaiNP2(+)	GGTCAGTTTCTATCCTTTGC	911-930	NP	GGUCAGUUUCUCUCCUUUGC	943-962	70	100	92.64	9
EBOLAID026 Raw data Min-max	PCR primer reverse	SudZaiNP2(-)	CATGTGTCCAACTGATTGCC	1041-1060	NP	GGCAAUCAGUAGGACACAUG	1073-1092	80	80	97.56	9
EBOLAID027 Raw data Min-max	PCR primer forward	EBsp5	TTYCCTAGCAAYATGATGG	13345-13363	L	UUUCCUAGCAAUAUGAUGG	13869-13887	78.95	100	95.93	10;4
EBOLAID028 Raw data Min-max	PCR primer reverse	EBsp3	TATAATAATCACTGACATGCAT	13600-13621	L	AUGCAUGUCAGUGAUUAUUAUA	14124-14145	90.91	80	98.11	10;4
EBOLAID029 Raw data Min-max	PCR primer forward	evR3	TCTTGCAAGGACCGCCAAGGTAAAAA	1267-1292	NP	UCUUGCAAGGACCGCCAAGGUAAAAA	1299-1324	50	20	88.54	11
EBOLAID030 Raw data Min-max	PCR primer reverse	evF3	TTCAAAAGTCGGGCGAAAGGAGCATA	1346-1371	NP	UAUGCUCCUUUCGCCCGACUUUUGAA	1378-1403	65.38	100	91.92	11
EBOLAID031 Raw data Min-max	PCR primer forward	F3	AATAACGAAAGGAGTCCCTA	18338-18357	3'UTR	AAUAACGAAAGGAGUCCCUA	18913-18932	0	0	73.31	12
EBOLAID032 Raw data Min-max	PCR primer reverse	B3	TTGTATCAATATCCTGTCAG	18532-18551	3'UTR	UUGUAUCAAUAUCCUGUCAG	19115-19129	0	0	76.44	12
EBOLAID033 Raw data Min-max	PCR primer forward	Ebola-1F	GATGCAGTATTCGAGCCTAATGTTCTAG	13063-13090	L	GAUGCAGUAUUCGAGCCUAAUGUUCUAG	13587-13614	67.86	40	94.04	13
EBOLAID034 Raw data Min-max	PCR primer reverse	Ebola-1R	GTGTTTGAACATTGCGAGTCGGATAAG	13280-13306	L	CUUAUCCGACUCGCAAUGUUCAAACAC	13804-13830	62.96	80	91.44	13
EBOLAID035 Raw data Min-max	Probe	Ebola-P	ACTCGAGTATCTACTACCACAATATCGGAA(...)	13191-13221	L	ACUCGAGUAUCUACUACCACAAUAUCGGAA(...)	13715-13745	38.71	60	89.67	13
EBOLAID036 Raw data Min-max	PCR primer forward	FiloA2.4	AAGCATTTCCTAGCAATATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13864-13888	76	100	95.3	7
EBOLAID037 Raw data Min-max	PCR primer forward	FiloA2.2	AAGCCTTTCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13864-13888	76	100	95.3	7
EBOLAID038 Raw data Min-max	PCR primer forward	FiloA2.3	AAGCATTCCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13864-13888	76	100	95.3	7
EBOLAID039 Raw data Min-max	PCR primer reverse	FILO B-Ra	GTGAGGAGGGCTATAAAAGTCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	14127-14145	94.74	100	98.3	7
EBOLAID040 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOSu	CCGAAATCATCACTIGTITGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13935-13957	78.26	100	97.68	7
EBOLAID041 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOg	CCAAAATCATCACTIGTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13935-13960	76.92	80	96.59	7
EBOLAID042 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMMBG	CCTATGCTTGCTGAATTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13935-13944	70	40	97.11	7
EBOLAID043 Raw data Min-max	PCR primer forward	F565	TCTGACATGGATTACCACAAGATC	518-541	NP	UCUGACAUGGAUUACCACAAGAUC	550-573	50	60	89.03	14
EBOLAID044 Raw data Min-max	PCR primer reverse	R640	GGATGACTCTTTGCCGAACAATC	571-593	NP	GAUUGUUCGGCAAAGAGUCAUCC	603-625	43.48	60	92.04	14
EBOLAID045 Raw data Min-max	Probe (FAM&MGB)	p597S	AGGTCTGTCCGTTCAA	550-565	NP	AGGUCUGUCCGUUCAA	582-597	50	60	89.71	14
EBOLAID046 Raw data Min-max	PCR primer forward	F2000	TTTTCAATCCTCAACCGTAAGGC	7781-7803	GP	UUUUCAAUCCUCAACCGUAAGGC	8013-8035	47.83	80	89.31	14
EBOLAID047 Raw data Min-max	PCR primer reverse	R2079	CAGTCCGGTCCCAGAATGTG	7841-7860	GP	CACAUUCUGGGACCGGACUG	8073-8092	45	40	87.92	14
EBOLAID048 Raw data Min-max	Probe (FAM&TAMRA)	p2058A	CATGTGCCGCCCCATCGCTGC	7819-7839	GP	GCAGCGAUGGGGCGGCACAUG	8051-8071	66.67	80	91.64	14
EBOLAID049 Raw data Min-max	PCR primer forward	PanFilo-L1	ATMGRAAYTTTTCYTTYTCWYT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	13738-13756	63.16	80	95.41	15
EBOLAID050 Raw data Min-max	PCR primer reverse	Pan?lo-L2	TGWGGHGGRYTATAAWARTCACTDACAT	13604-13631	L	AUGUCAGUGAUUAUUAUAAUCCACCACA	14128-14155	85.71	80	96.04	15
EBOLAID051 Raw data Min-max	PCR primer forward	PanFilo-L3	GCNAARGCMTTYCCHAGYAAYATGATGG	13336-13363	L	GCUAAAGCAUUUCCUAGCAAUAUGAUGG	13863-13887	76	100	95.3	15
EBOLAID052 Raw data Min-max	PCR primer reverse	Pan?lo-L4	ATAAWARTCACTDACATGCATRTARCA	13594-13620	L	UGUUAUAUGCAUGUCAGUGAUUAUUAU	14118-14144	88.89	100	97.58	15
EBOLAID053 Raw data Min-max	PCR primer forward	KGH-F	GTCGTTCCAACAATCGAGCG	10243-10262	VP24	GUCGUUCCAACAAUCGAGCG	10684-10703	0	0	76.56	16
EBOLAID054 Raw data Min-max	PCR primer forward	KGH-R	CGTCCCGTAGCTTTRGCCAT	10345-10364	VP24	AUGGCUAAAGCUACGGGACG	10789-10808	70	60	92.16	16
EBOLAID055 Raw data Min-max	PCR primer forward	ZEBOV-F	TGGAAAAAACATTAAGAGAACACTTGC	847-873	NP	UGGAAAAAACAUUAAGAGAACACUUGC	879-905	51.85	60	89.95	17
EBOLAID056 Raw data Min-max	PCR primer reverse	ZEBOV-R	AGGAGAGAAACTGACCGGCAT	906-926	NP	AUGCCGGUCAGUUUCUCUCCU	938-958	66.67	80	91.53	17
EBOLAID057 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	ZEBOV-P	CATGCCGGAAGAGGAGACAACTGAAGC	877-903	NP	CAUGCCGGAAGAGGAGACAACUGAAGC	909-935	74.07	100	93.97	17
EBOLAID058 Raw data Min-max	PCR primer forward	rt_EBOV-f	ATTTGAATGGGGTCCAATTGCC	13997-14018	L	AUUUGAAUGGGGUCCAAUUGCC	14521-14542	63.64	80	92.55	22
EBOLAID059 Raw data Min-max	PCR primer reverse	rt_EBOL-r	AAGCAGTRCCTATACTAGCCA	14090-14110	L	UGGCUAGUAUAGGCACUGCUU	14614-14634	66.67	60	92.31	22
EBOLAID060 Raw data Min-max	Probe (Taqman)	EBOV_prb	AGTCCCTTAAAACGGCTACAAGAATGGGAC	14021-14050	L	AGUCCCUUAAAACGGCUACAAGAAUGGCAC	14545-14571	62.96	60	90.86	22
EBOLAID061 Raw data Min-max	Primer forward	F3	GACGGGAGTGAGTGTCTACC	6387-6406	GP	GACGGGAGUGAGUGUCUACC	6582-6601	65	60	93.37	23
EBOLAID062 Raw data Min-max	Primer reverse	B3	AGCTTGGGGCAGTATCAGAA	6586-6605	GP	UUCUGAUACUGCCCCAAGCU	6781-6800	40	40	86.88	23
EBOLAID063 Raw data Min-max	Primer reverse	FL	GCACATACCGGCACC	6439-6453	GP	GGUGCCGGUAUGUGC	6634-6648	73.33	60	94.48	23
EBOLAID064 Raw data Min-max	Primer forward	BL	CTTCCTGTATGATCGACTTGCTTC	6515-6538	GP	CUUCCUGUAUGAUCGACUUGCUUC	6710-6733	58.33	80	93.17	23
EBOLAID065 Raw data Min-max	Primer forward	F3	CAATAAACAACTATTTAAATAAC	18321-18343	3'UTR	CAAUAAACAACUAUUUAAAUAAC	18896-18918	0	0	77.38	24
EBOLAID066 Raw data Min-max	Primer reverse	B3	CTGGCAAGATATTGATACAACA	18530-18551	3'UTR	UGUUGUAUCAAUAUCCUGUCAG	7074-7085	25	40	83.44	24
EBOLAID067 Raw data Min-max	Primer reverse	LF	AATTTTTTGATTATCACGC	18388-18406	3'UTR	GCGUGAUAAUCAAAAAAUU	18963-18981	5.26	20	81.11	24
EBOLAID068 Raw data Min-max	Primer forward	F3	TGAAGTCAAGAAGCGTGATGG	787-807	NP	UGAAGUCAAGAAGCGUGAUGG	819-839	33.33	40	83.89	24
EBOLAID069 Raw data Min-max	Primer reverse	B3	AGTCCTTGCTCTGCATGTACT	1000-1020	NP	AGUACAUGCAGAGCAAGGACU	1032-1052	57.14	60	92.81	24
EBOLAID070 Raw data Min-max	Primer reverse	LF	TGTTTTTTCCACTAGATACTGCTGG	833-857	NP	CCAGCAGUAUCUAGUGGAAAAAACA	865-889	40	40	86.52	24
EBOLAID071 Raw data Min-max	Primer forward	LB	TCCTTCCGAAATTGGTAGTAGGA	939-961	NP	UCCUUCCGAAAUUGGUAGUAGGA	971-993	60.87	60	90.99	24
EBOLAID072 Raw data Min-max	Primer forward	EBOV-F3	TGGTTCAAGTGCACAGTCAA	7086-7105	GP	UGGUUCAAGUGCACAGUCAA	7281-7300	40	0	89.64	25
EBOLAID073 Raw data Min-max	Primer reverse	EBOV-B3	TGTCTGCTCTACGGTGATGT	7255-7274	GP	ACAUCACCGCAGAACAGACA	7450-7469	10	20	81.73	25
EBOLAID074 Raw data Min-max	Primer reverse	EBOV-LF	GCAAGGGTTGTCAGATGCG	7125-7143	GP	CGCAUCUAACAACCCUUGC	7320-7338	10.53	20	83.66	25
EBOLAID075 Raw data Min-max	Primer forward	EBOV-LB	ATAATACACCCGTGTATAAACTTGAC	7203-7228	GP	AUAAUACACCCGUGUAUAAACUUGAC	7398-7423	7.69	0	85.14	25
EBOLAID076 Raw data Min-max	PCR primer forward	ZEBOV Forward	CGAACTTGACCATCTTGGACTTG	1552-1574	NP	CGAACUUGACCAUCUUGGACUUG	1584-1606	52.17	60	89.85	26
EBOLAID077 Raw data Min-max	PCR primer reverse	ZEBOV Reverse	TCCTCGTCGTCCTCGTCTAGAT	1929-1950	NP	AUCUAGACGAGGACGACGAGGA	1961-1982	50	40	90.56	26
EBOLAID078 Raw data Min-max	Primer forward	EBO-RPA-F	TAGTAGGAGAAAAGGCTTGCCTTGAGAAGG(...)	954-983	NP	UAGUAGGAGAAAAGGCUUGCCUUGAGAAGG	986-1015	63.33	60	91.45	27
EBOLAID079 Raw data Min-max	Primer reverse	EBO-RPA-R	TGTTCGCATCAAACGGAAAATCACCATCAT(...)	1057-1087	NP	CAUGAUGGUGAUUUUCCGUUUGAUGCGAAC(...)	1089-1119	64.52	80	94.38	27
EBOLAID080 Raw data Min-max	Probe	EBO-RPA-P	TCAAGTACATGCAGAGCAAGGACTGATACA(...)	997-1028	NP	UCAAGUACAUGCAGAGCAAGGACUGAUACA(...)	1029-1060	62.5	80	93.23	27