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_alig05
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	7661-7682	31.82	60	93.98	1
EBOLAID002 Raw data Min-max	PCR primer reverse	EBO-2	ACGACACCTTCAGCRAAAGT	6561-6580	GP	ACUUUCGCUGAAGGUGUCGU	8144-8163	40	40	92.18	1
EBOLAID003 Raw data Min-max	PCR primer forward	EBO-3	GTTTGTCGKGACAAACTGTC	6192-6211	GP	GUUUGUCGUGACAAACUGUC	7763-7782	0	0	90	1
EBOLAID004 Raw data Min-max	PCR primer reverse	EBO-4	TGGAARGCWAAGTCWCCGG	6481-6499	GP	CCGGAGACUUUGCCUUCCA	8064-8082	42.11	40	91.6	1
EBOLAID005 Raw data Min-max	PCR primer forward	GAB-1	GAATGTAGGTAGAACCTTCGG	13251-13271	L	GAAUGUAGGUAGAACCUUCGG	17400-17420	52.38	80	90.17	1
EBOLAID006 Raw data Min-max	PCR primer reverse	GAB-2	GCATATAACACTGTGGGATTG	13583-13603	L	CAAUCCCACAGUGUUAUAUGC	17738-17758	57.14	40	93.59	1
EBOLAID007 Raw data Min-max	PCR primer forward	EBO-BP1	AATGGGCTGAAAATTGCTACAATC	6346-6369	GP	AAUGGGCUGAAAACUGCUACAAUC	7926-7949	45.83	40	96.72	2
EBOLAID008 Raw data Min-max	PCR primer reverse	EBO-GP2	TTTTTTTAGTTTCCCAGAAGGCCCACT	6898-6924	GP	AGUGGGCCUUCUGGGAAACUAAAAAAA	8545-8571	25.93	40	96.56	2
EBOLAID009 Raw data Min-max	PCR primer forward	ZAI-NP1	GGACCGCCAAGGTAAAAAATGA	1275-1296	NP	GGACCGCCAAGGUAAAAAAUGA	1605-1626	54.55	80	91.92	2
EBOLAID010 Raw data Min-max	PCR primer reverse	ZAI-NP2	GCATATTGTTGGAGTTGCTTCTCAGC	1517-1542	NP	GCUGAGAAGCAACUCCAACAAUAUGC	1847-1872	30.77	80	95.01	2
EBOLAID011 Raw data Min-max	PCR primer forward		ATCGGAATTTTCTTTCTCATTGAAAGA	13214-13241	L	AUCGGAACUUUUCUUUCUCAUUGAAAGA	17363-17390	60.71	80	93.96	3;4
EBOLAID012 Raw data Min-max	PCR primer reverse		ATGTGGTGGATTATAATAATCACTGACATG(...)	13600-13632	L	AUGCAUGUCAGUGAUUAUUAUAAUCCACCA(...)	17755-17787	72.73	80	95.64	3;4
EBOLAID013 Raw data Min-max	PCR primer forward	EBOGP-1Df	TGGGCTGAAAAYTGCTACAATC	6348-6369	GP	UGGGCUGAAAACUGCUACAAUC	7928-7949	45.45	40	96.8	5
EBOLAID014 Raw data Min-max	PCR primer reverse	EBOGP-1Dr	CTTTGTGMACATASCGGCAC	6440-6459	GP	GUGCCGGUAUGUGCACAAAG	8020-8039	35	40	94.15	5
EBOLAID015 Raw data Min-max	Probe	EBOGP-1DZPrb	CTACCAGCAGCGCCAGACGG	6402-6421	GP	CUACCAGCAGCGCCAGACGG	7982-8001	20	0	89.07	5
EBOLAID016 Raw data Min-max	PCR primer forward	FILO-A	ATCGGAATTTTTCTTTCTCATT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	17363-17384	59.09	60	94.17	2;1;5;6
EBOLAID017 Raw data Min-max	PCR primer reverse	FILO-B	ATGTGGTGGGTTATAATAATCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	17758-17787	73.33	100	95.53	2;1;5;6;7
EBOLAID018 Raw data Min-max	PCR primer forward	EBOORF UP	ATGGATTCTCGTCCTCAGAAAAT	470-492	NP	AUGGAUUCUCGUCCUCAGAAAAU	731-753	21.74	40	87.47	8
EBOLAID019 Raw data Min-max	PCR primer reverse	EBOORF DP	TCACTGATGATGTTGCAGGATT	2668-2689	NP	AAUCCUGCAACAUCAUCAGUGA	3201-3222	31.82	20	92.76	8
EBOLAID020 Raw data Min-max	PCR primer forward	ENZ FP	ATGATGGAAGCTACGGCG	1854-1871	NP	AUGAUGGAAGCUACGGCG	2199-2216	16.67	0	81.96	8
EBOLAID021 Raw data Min-max	PCR primer reverse	ENZ RP	AGGACCAAGTCATCTGGTGC	1904-1923	NP	GCACCAGAUGACUUGGUCCU	2257-2272	12.5	20	90.46	8
EBOLAID022 Raw data Min-max	Probe	ENZ P	CCAGAGTTACTCGGAAAACGGCATG	1876-1900	NP	CCAGAGUUACUCGGAAAACGGCAUG	2221-2247	3.7	0	81.46	8
EBOLAID023 Raw data Min-max	PCR primer forward	SudZaiNP1(+)	GAGACAACGGAAGCTAATGC	890-909	NP	GAGACAACUGAAGCUAAUGC	1211-1225	13.33	60	92.65	9
EBOLAID024 Raw data Min-max	PCR primer reverse	SudZaiNP1(-)	AACGGAAGATCACCATCATG	1057-1076	NP	CAUGAUGGUGAUUUUCCGUU	1387-1406	55	80	93.92	9
EBOLAID025 Raw data Min-max	PCR primer forward	SudZaiNP2(+)	GGTCAGTTTCTATCCTTTGC	911-930	NP	GGUCAGUUUCUCUCCUUUGC	1241-1260	55	60	92.09	9
EBOLAID026 Raw data Min-max	PCR primer reverse	SudZaiNP2(-)	CATGTGTCCAACTGATTGCC	1041-1060	NP	GGCAAUCAGUAGGACACAUG	1371-1390	55	60	96.78	9
EBOLAID027 Raw data Min-max	PCR primer forward	EBsp5	TTYCCTAGCAAYATGATGG	13345-13363	L	UUUCCUAGCAAUAUGAUGG	17494-17512	78.95	100	95.79	10;4
EBOLAID028 Raw data Min-max	PCR primer reverse	EBsp3	TATAATAATCACTGACATGCAT	13600-13621	L	AUGCAUGUCAGUGAUUAUUAUA	17755-17776	81.82	80	97.94	10;4
EBOLAID029 Raw data Min-max	PCR primer forward	evR3	TCTTGCAAGGACCGCCAAGGTAAAAA	1267-1292	NP	UCUUGCAAGGACCGCCAAGGUAAAAA	1597-1622	42.31	20	88.54	11
EBOLAID030 Raw data Min-max	PCR primer reverse	evF3	TTCAAAAGTCGGGCGAAAGGAGCATA	1346-1371	NP	UAUGCUCCUUUCGCCCGACUUUUGAA	1676-1701	61.54	80	91.73	11
EBOLAID031 Raw data Min-max	PCR primer forward	F3	AATAACGAAAGGAGTCCCTA	18338-18357	3'UTR	AAUAACGAAAGGAGUCCCUA	1680-1688	66.67	60	92.39	12
EBOLAID032 Raw data Min-max	PCR primer reverse	B3	TTGTATCAATATCCTGTCAG	18532-18551	3'UTR	UUGUAUCAAUAUCCUGUCAG	23604-23629	0	0	83.92	12
EBOLAID033 Raw data Min-max	PCR primer forward	Ebola-1F	GATGCAGTATTCGAGCCTAATGTTCTAG	13063-13090	L	GAUGCAGUAUUCGAGCCUAAUGUUCUAG	17212-17239	46.43	40	93.12	13
EBOLAID034 Raw data Min-max	PCR primer reverse	Ebola-1R	GTGTTTGAACATTGCGAGTCGGATAAG	13280-13306	L	CUUAUCCGACUCGCAAUGUUCAAACAC	17429-17455	55.56	80	91.23	13
EBOLAID035 Raw data Min-max	Probe	Ebola-P	ACTCGAGTATCTACTACCACAATATCGGAA(...)	13191-13221	L	ACUCGAGUAUCUACUACCACAAUAUCGGAA(...)	17340-17370	32.26	60	89.1	13
EBOLAID036 Raw data Min-max	PCR primer forward	FiloA2.4	AAGCATTTCCTAGCAATATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	17489-17513	76	100	95.23	7
EBOLAID037 Raw data Min-max	PCR primer forward	FiloA2.2	AAGCCTTTCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	17489-17513	76	100	95.23	7
EBOLAID038 Raw data Min-max	PCR primer forward	FiloA2.3	AAGCATTCCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	17489-17513	76	100	95.23	7
EBOLAID039 Raw data Min-max	PCR primer reverse	FILO B-Ra	GTGAGGAGGGCTATAAAAGTCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	17758-17776	84.21	100	98.12	7
EBOLAID040 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOSu	CCGAAATCATCACTIGTITGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	17578-17588	27.27	20	99	7
EBOLAID041 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOg	CCAAAATCATCACTIGTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	17578-17591	35.71	60	96.4	7
EBOLAID042 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMMBG	CCTATGCTTGCTGAATTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	17560-17569	70	40	97.04	7
EBOLAID043 Raw data Min-max	PCR primer forward	F565	TCTGACATGGATTACCACAAGATC	518-541	NP	UCUGACAUGGAUUACCACAAGAUC	813-836	50	60	89.46	14
EBOLAID044 Raw data Min-max	PCR primer reverse	R640	GGATGACTCTTTGCCGAACAATC	571-593	NP	GAUUGUUCGGCAAAGAGUCAUCC	866-888	26.09	40	91.06	14
EBOLAID045 Raw data Min-max	Probe (FAM&MGB)	p597S	AGGTCTGTCCGTTCAA	550-565	NP	AGGUCUGUCCGUUCAA	845-860	43.75	60	90.08	14
EBOLAID046 Raw data Min-max	PCR primer forward	F2000	TTTTCAATCCTCAACCGTAAGGC	7781-7803	GP	UUUUCAAUCCUCAACCGUAAGGC	9938-9960	43.48	60	88.95	14
EBOLAID047 Raw data Min-max	PCR primer reverse	R2079	CAGTCCGGTCCCAGAATGTG	7841-7860	GP	CACAUUCUGGGACCGGACUG	9998-10017	40	20	87.6	14
EBOLAID048 Raw data Min-max	Probe (FAM&TAMRA)	p2058A	CATGTGCCGCCCCATCGCTGC	7819-7839	GP	GCAGCGAUGGGGCGGCACAUG	9976-9996	57.14	80	91.19	14
EBOLAID049 Raw data Min-max	PCR primer forward	PanFilo-L1	ATMGRAAYTTTTCYTTYTCWYT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	17363-17381	63.16	80	94.82	15
EBOLAID050 Raw data Min-max	PCR primer reverse	Pan?lo-L2	TGWGGHGGRYTATAAWARTCACTDACAT	13604-13631	L	AUGUCAGUGAUUAUUAUAAUCCACCACA	17759-17786	75	80	95.63	15
EBOLAID051 Raw data Min-max	PCR primer forward	PanFilo-L3	GCNAARGCMTTYCCHAGYAAYATGATGG	13336-13363	L	GCUAAAGCAUUUCCUAGCAAUAUGAUGG	17488-17512	76	100	95.23	15
EBOLAID052 Raw data Min-max	PCR primer reverse	Pan?lo-L4	ATAAWARTCACTDACATGCATRTARCA	13594-13620	L	UGUUAUAUGCAUGUCAGUGAUUAUUAU	17749-17775	77.78	80	97.46	15
EBOLAID053 Raw data Min-max	PCR primer forward	KGH-F	GTCGTTCCAACAATCGAGCG	10243-10262	VP24	GUCGUUCCAACAAUCGAGCG	13481-13528	2.08	0	86.09	16
EBOLAID054 Raw data Min-max	PCR primer forward	KGH-R	CGTCCCGTAGCTTTRGCCAT	10345-10364	VP24	AUGGCUAAAGCUACGGGACG	13740-13759	40	20	91.79	16
EBOLAID055 Raw data Min-max	PCR primer forward	ZEBOV-F	TGGAAAAAACATTAAGAGAACACTTGC	847-873	NP	UGGAAAAAACAUUAAGAGAACACUUGC	1163-1190	17.86	20	89.42	17
EBOLAID056 Raw data Min-max	PCR primer reverse	ZEBOV-R	AGGAGAGAAACTGACCGGCAT	906-926	NP	AUGCCGGUCAGUUUCUCUCCU	1236-1256	42.86	0	90.89	17
EBOLAID057 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	ZEBOV-P	CATGCCGGAAGAGGAGACAACTGAAGC	877-903	NP	CAUGCCGGAAGAGGAGACAACUGAAGC	1194-1224	19.35	80	93.43	17
EBOLAID058 Raw data Min-max	PCR primer forward	rt_EBOV-f	ATTTGAATGGGGTCCAATTGCC	13997-14018	L	AUUUGAAUGGGGUCCAAUUGCC	18154-18175	59.09	60	92.5	22
EBOLAID059 Raw data Min-max	PCR primer reverse	rt_EBOL-r	AAGCAGTRCCTATACTAGCCA	14090-14110	L	UGGCUAGUAUAGGCACUGCUU	18247-18267	61.9	60	91.7	22
EBOLAID060 Raw data Min-max	Probe (Taqman)	EBOV_prb	AGTCCCTTAAAACGGCTACAAGAATGGGAC	14021-14050	L	AGUCCCUUAAAACGGCUACAAGAAUGGCAC	18178-18204	44.44	20	90.34	22
EBOLAID061 Raw data Min-max	Primer forward	F3	GACGGGAGTGAGTGTCTACC	6387-6406	GP	GACGGGAGUGAGUGUCUACC	7967-7986	25	20	92.13	23
EBOLAID062 Raw data Min-max	Primer reverse	B3	AGCTTGGGGCAGTATCAGAA	6586-6605	GP	UUCUGAUACUGCCCCAAGCU	8169-8181	23.08	20	90.09	23
EBOLAID063 Raw data Min-max	Primer reverse	FL	GCACATACCGGCACC	6439-6453	GP	GGUGCCGGUAUGUGC	8019-8033	33.33	40	93.18	23
EBOLAID064 Raw data Min-max	Primer forward	BL	CTTCCTGTATGATCGACTTGCTTC	6515-6538	GP	CUUCCUGUAUGAUCGACUUGCUUC	8098-8121	58.33	80	93.16	23
EBOLAID065 Raw data Min-max	Primer forward	F3	CAATAAACAACTATTTAAATAAC	18321-18343	3'UTR	CAAUAAACAACUAUUUAAAUAAC	23260-23269	0	0	81.84	24
EBOLAID066 Raw data Min-max	Primer reverse	B3	CTGGCAAGATATTGATACAACA	18530-18551	3'UTR	UGUUGUAUCAAUAUCCUGUCAG	8526-8537	25	40	84.08	24
EBOLAID067 Raw data Min-max	Primer reverse	LF	AATTTTTTGATTATCACGC	18388-18406	3'UTR	GCGUGAUAAUCAAAAAAUU	7954-7963	30	40	90.73	24
EBOLAID068 Raw data Min-max	Primer forward	F3	TGAAGTCAAGAAGCGTGATGG	787-807	NP	UGAAGUCAAGAAGCGUGAUGG	1083-1103	23.81	0	84.08	24
EBOLAID069 Raw data Min-max	Primer reverse	B3	AGTCCTTGCTCTGCATGTACT	1000-1020	NP	AGUACAUGCAGAGCAAGGACU	1330-1350	52.38	60	92.33	24
EBOLAID070 Raw data Min-max	Primer reverse	LF	TGTTTTTTCCACTAGATACTGCTGG	833-857	NP	CCAGCAGUAUCUAGUGGAAAAAACA	1149-1173	12	40	86.48	24
EBOLAID071 Raw data Min-max	Primer forward	LB	TCCTTCCGAAATTGGTAGTAGGA	939-961	NP	UCCUUCCGAAAUUGGUAGUAGGA	1269-1291	60.87	60	91.01	24
EBOLAID072 Raw data Min-max	Primer forward	EBOV-F3	TGGTTCAAGTGCACAGTCAA	7086-7105	GP	UGGUUCAAGUGCACAGUCAA	8793-8807	26.67	0	93.38	25
EBOLAID073 Raw data Min-max	Primer reverse	EBOV-B3	TGTCTGCTCTACGGTGATGT	7255-7274	GP	ACAUCACCGCAGAACAGACA	9082-9090	0	0	85.47	25
EBOLAID074 Raw data Min-max	Primer reverse	EBOV-LF	GCAAGGGTTGTCAGATGCG	7125-7143	GP	CGCAUCUAACAACCCUUGC	8850-8865	0	20	85.48	25
EBOLAID075 Raw data Min-max	Primer forward	EBOV-LB	ATAATACACCCGTGTATAAACTTGAC	7203-7228	GP	AUAAUACACCCGUGUAUAAACUUGAC	9036-9047	0	0	88.11	25
EBOLAID076 Raw data Min-max	PCR primer forward	ZEBOV Forward	CGAACTTGACCATCTTGGACTTG	1552-1574	NP	CGAACUUGACCAUCUUGGACUUG	1882-1906	16	20	89.29	26
EBOLAID077 Raw data Min-max	PCR primer reverse	ZEBOV Reverse	TCCTCGTCGTCCTCGTCTAGAT	1929-1950	NP	AUCUAGACGAGGACGACGAGGA	2278-2299	22.73	20	90.69	26
EBOLAID078 Raw data Min-max	Primer forward	EBO-RPA-F	TAGTAGGAGAAAAGGCTTGCCTTGAGAAGG(...)	954-983	NP	UAGUAGGAGAAAAGGCUUGCCUUGAGAAGG	1284-1313	53.33	60	91.24	27
EBOLAID079 Raw data Min-max	Primer reverse	EBO-RPA-R	TGTTCGCATCAAACGGAAAATCACCATCAT(...)	1057-1087	NP	CAUGAUGGUGAUUUUCCGUUUGAUGCGAAC(...)	1387-1417	48.39	80	93.62	27
EBOLAID080 Raw data Min-max	Probe	EBO-RPA-P	TCAAGTACATGCAGAGCAAGGACTGATACA(...)	997-1028	NP	UCAAGUACAUGCAGAGCAAGGACUGAUACA(...)	1327-1358	43.75	40	92.48	27