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_alig02
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	6102-6121	100	100	100	1
EBOLAID002 Raw data Min-max	PCR primer reverse	EBO-2	ACGACACCTTCAGCRAAAGT	6561-6580	GP	ACUUUCGCUGAAGGUGUCGU	6561-6580	100	100	100	1
EBOLAID003 Raw data Min-max	PCR primer forward	EBO-3	GTTTGTCGKGACAAACTGTC	6192-6211	GP	GUUUGUCGUGACAAACUGUC	6192-6211	95	100	99.35	1
EBOLAID004 Raw data Min-max	PCR primer reverse	EBO-4	TGGAARGCWAAGTCWCCGG	6481-6499	GP	CCGGAGACUUUGCCUUCCA	6481-6499	100	100	100	1
EBOLAID005 Raw data Min-max	PCR primer forward	GAB-1	GAATGTAGGTAGAACCTTCGG	13251-13271	L	GAAUGUAGGUAGAACCUUCGG	13251-13271	90.48	100	98.96	1
EBOLAID006 Raw data Min-max	PCR primer reverse	GAB-2	GCATATAACACTGTGGGATTG	13583-13603	L	CAAUCCCACAGUGUUAUAUGC	13583-13603	95.24	100	99.91	1
EBOLAID007 Raw data Min-max	PCR primer forward	EBO-BP1	AATGGGCTGAAAATTGCTACAATC	6346-6369	GP	AAUGGGCUGAAAACUGCUACAAUC	6346-6369	100	100	100	2
EBOLAID008 Raw data Min-max	PCR primer reverse	EBO-GP2	TTTTTTTAGTTTCCCAGAAGGCCCACT	6898-6924	GP	AGUGGGCCUUCUGGGAAACUAAAAAAA	6898-6924	96.3	100	99.93	2
EBOLAID009 Raw data Min-max	PCR primer forward	ZAI-NP1	GGACCGCCAAGGTAAAAAATGA	1275-1296	NP	GGACCGCCAAGGUAAAAAAUGA	1275-1296	86.36	100	99.73	2
EBOLAID010 Raw data Min-max	PCR primer reverse	ZAI-NP2	GCATATTGTTGGAGTTGCTTCTCAGC	1517-1542	NP	GCUGAGAAGCAACUCCAACAAUAUGC	1517-1542	96.15	100	99.5	2
EBOLAID011 Raw data Min-max	PCR primer forward		ATCGGAATTTTCTTTCTCATTGAAAGA	13214-13241	L	AUCGGAACUUUUCUUUCUCAUUGAAAGA	13214-13241	92.86	100	99.29	3;4
EBOLAID012 Raw data Min-max	PCR primer reverse		ATGTGGTGGATTATAATAATCACTGACATG(...)	13600-13632	L	AUGCAUGUCAGUGAUUAUUAUAAUCCACCA(...)	13600-13632	96.97	100	99.45	3;4
EBOLAID013 Raw data Min-max	PCR primer forward	EBOGP-1Df	TGGGCTGAAAAYTGCTACAATC	6348-6369	GP	UGGGCUGAAAACUGCUACAAUC	6348-6369	100	100	100	5
EBOLAID014 Raw data Min-max	PCR primer reverse	EBOGP-1Dr	CTTTGTGMACATASCGGCAC	6440-6459	GP	GUGCCGGUAUGUGCACAAAG	6440-6459	100	100	100	5
EBOLAID015 Raw data Min-max	Probe	EBOGP-1DZPrb	CTACCAGCAGCGCCAGACGG	6402-6421	GP	CUACCAGCAGCGCCAGACGG	6402-6421	100	100	100	5
EBOLAID016 Raw data Min-max	PCR primer forward	FILO-A	ATCGGAATTTTTCTTTCTCATT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	13214-13235	90.91	100	99.09	2;1;5;6
EBOLAID017 Raw data Min-max	PCR primer reverse	FILO-B	ATGTGGTGGGTTATAATAATCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	13603-13632	96.67	100	99.4	2;1;5;6;7
EBOLAID018 Raw data Min-max	PCR primer forward	EBOORF UP	ATGGATTCTCGTCCTCAGAAAAT	470-492	NP	AUGGAUUCUCGUCCUCAGAAAAU	470-492	95.65	80	99.75	8
EBOLAID019 Raw data Min-max	PCR primer reverse	EBOORF DP	TCACTGATGATGTTGCAGGATT	2668-2689	NP	AAUCCUGCAACAUCAUCAGUGA	2668-2689	95.45	80	99.91	8
EBOLAID020 Raw data Min-max	PCR primer forward	ENZ FP	ATGATGGAAGCTACGGCG	1854-1871	NP	AUGAUGGAAGCUACGGCG	1854-1871	94.44	100	98.22	8
EBOLAID021 Raw data Min-max	PCR primer reverse	ENZ RP	AGGACCAAGTCATCTGGTGC	1904-1923	NP	GCACCAGAUGACUUGGUCCU	1904-1923	90	100	99.7	8
EBOLAID022 Raw data Min-max	Probe	ENZ P	CCAGAGTTACTCGGAAAACGGCATG	1876-1900	NP	CCAGAGUUACUCGGAAAACGGCAUG	1876-1900	92	80	98.06	8
EBOLAID023 Raw data Min-max	PCR primer forward	SudZaiNP1(+)	GAGACAACGGAAGCTAATGC	890-909	NP	GAGACAACUGAAGCUAAUGC	890-909	90	100	98.9	9
EBOLAID024 Raw data Min-max	PCR primer reverse	SudZaiNP1(-)	AACGGAAGATCACCATCATG	1057-1076	NP	CAUGAUGGUGAUUUUCCGUU	1057-1076	100	100	100	9
EBOLAID025 Raw data Min-max	PCR primer forward	SudZaiNP2(+)	GGTCAGTTTCTATCCTTTGC	911-930	NP	GGUCAGUUUCUCUCCUUUGC	911-930	85	100	97.48	9
EBOLAID026 Raw data Min-max	PCR primer reverse	SudZaiNP2(-)	CATGTGTCCAACTGATTGCC	1041-1060	NP	GGCAAUCAGUAGGACACAUG	1041-1060	100	100	100	9
EBOLAID027 Raw data Min-max	PCR primer forward	EBsp5	TTYCCTAGCAAYATGATGG	13345-13363	L	UUUCCUAGCAAUAUGAUGG	13345-13363	100	100	100	10;4
EBOLAID028 Raw data Min-max	PCR primer reverse	EBsp3	TATAATAATCACTGACATGCAT	13600-13621	L	AUGCAUGUCAGUGAUUAUUAUA	13600-13621	100	100	100	10;4
EBOLAID029 Raw data Min-max	PCR primer forward	evR3	TCTTGCAAGGACCGCCAAGGTAAAAA	1267-1292	NP	UCUUGCAAGGACCGCCAAGGUAAAAA	1267-1292	88.46	80	99.77	11
EBOLAID030 Raw data Min-max	PCR primer reverse	evF3	TTCAAAAGTCGGGCGAAAGGAGCATA	1346-1371	NP	UAUGCUCCUUUCGCCCGACUUUUGAA	1346-1371	100	100	100	11
EBOLAID031 Raw data Min-max	PCR primer forward	F3	AATAACGAAAGGAGTCCCTA	18338-18357	3'UTR	AAUAACGAAAGGAGUCCCUA	18338-18357	70	80	94.86	12
EBOLAID032 Raw data Min-max	PCR primer reverse	B3	TTGTATCAATATCCTGTCAG	18532-18551	3'UTR	UUGUAUCAAUAUCCUGUCAG	18532-18551	80	80	95.76	12
EBOLAID033 Raw data Min-max	PCR primer forward	Ebola-1F	GATGCAGTATTCGAGCCTAATGTTCTAG	13063-13090	L	GAUGCAGUAUUCGAGCCUAAUGUUCUAG	13063-13090	96.43	80	98.85	13
EBOLAID034 Raw data Min-max	PCR primer reverse	Ebola-1R	GTGTTTGAACATTGCGAGTCGGATAAG	13280-13306	L	CUUAUCCGACUCGCAAUGUUCAAACAC	13280-13306	100	100	100	13
EBOLAID035 Raw data Min-max	Probe	Ebola-P	ACTCGAGTATCTACTACCACAATATCGGAA(...)	13191-13221	L	ACUCGAGUAUCUACUACCACAAUAUCGGAA(...)	13191-13221	90.32	80	99.17	13
EBOLAID036 Raw data Min-max	PCR primer forward	FiloA2.4	AAGCATTTCCTAGCAATATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13340-13364	100	100	100	7
EBOLAID037 Raw data Min-max	PCR primer forward	FiloA2.2	AAGCCTTTCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13340-13364	100	100	100	7
EBOLAID038 Raw data Min-max	PCR primer forward	FiloA2.3	AAGCATTCCCTAGCAACATGATGGT	13340-13364	L	AAGCAUUUCCUAGCAAUAUGAUGGU	13340-13364	100	100	100	7
EBOLAID039 Raw data Min-max	PCR primer reverse	FILO B-Ra	GTGAGGAGGGCTATAAAAGTCACTGACATG	13603-13632	L	CAUGUCAGUGAUUAUUAUAAUCCACCACAU	13603-13621	100	100	100	7
EBOLAID040 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOSu	CCGAAATCATCACTIGTITGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13411-13433	91.3	100	99.66	7
EBOLAID041 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMEBOg	CCAAAATCATCACTIGTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13411-13436	88.46	80	98.47	7
EBOLAID042 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	FAMMBG	CCTATGCTTGCTGAATTGTGGTGCCA	13411-13436	L	UGGCACCACACAAGUGAUGAUUUUGG	13411-13420	90	80	99.42	7
EBOLAID043 Raw data Min-max	PCR primer forward	F565	TCTGACATGGATTACCACAAGATC	518-541	NP	UCUGACAUGGAUUACCACAAGAUC	518-541	100	100	100	14
EBOLAID044 Raw data Min-max	PCR primer reverse	R640	GGATGACTCTTTGCCGAACAATC	571-593	NP	GAUUGUUCGGCAAAGAGUCAUCC	571-593	95.65	80	99.91	14
EBOLAID045 Raw data Min-max	Probe (FAM&MGB)	p597S	AGGTCTGTCCGTTCAA	550-565	NP	AGGUCUGUCCGUUCAA	550-565	100	100	100	14
EBOLAID046 Raw data Min-max	PCR primer forward	F2000	TTTTCAATCCTCAACCGTAAGGC	7781-7803	GP	UUUUCAAUCCUCAACCGUAAGGC	7781-7803	100	100	100	14
EBOLAID047 Raw data Min-max	PCR primer reverse	R2079	CAGTCCGGTCCCAGAATGTG	7841-7860	GP	CACAUUCUGGGACCGGACUG	7841-7860	90	80	98.89	14
EBOLAID048 Raw data Min-max	Probe (FAM&TAMRA)	p2058A	CATGTGCCGCCCCATCGCTGC	7819-7839	GP	GCAGCGAUGGGGCGGCACAUG	7819-7839	95.24	100	98.47	14
EBOLAID049 Raw data Min-max	PCR primer forward	PanFilo-L1	ATMGRAAYTTTTCYTTYTCWYT	13214-13235	L	AUCGGAACUUUUCUUUCUCAUU	13214-13232	89.47	100	98.95	15
EBOLAID050 Raw data Min-max	PCR primer reverse	Pan?lo-L2	TGWGGHGGRYTATAAWARTCACTDACAT	13604-13631	L	AUGUCAGUGAUUAUUAUAAUCCACCACA	13604-13631	96.43	100	99.36	15
EBOLAID051 Raw data Min-max	PCR primer forward	PanFilo-L3	GCNAARGCMTTYCCHAGYAAYATGATGG	13336-13363	L	GCUAAAGCAUUUCCUAGCAAUAUGAUGG	13339-13363	100	100	100	15
EBOLAID052 Raw data Min-max	PCR primer reverse	Pan?lo-L4	ATAAWARTCACTDACATGCATRTARCA	13594-13620	L	UGUUAUAUGCAUGUCAGUGAUUAUUAU	13594-13620	100	100	100	15
EBOLAID053 Raw data Min-max	PCR primer forward	KGH-F	GTCGTTCCAACAATCGAGCG	10243-10262	VP24	GUCGUUCCAACAAUCGAGCG	10243-10262	90	100	99.8	16
EBOLAID054 Raw data Min-max	PCR primer forward	KGH-R	CGTCCCGTAGCTTTRGCCAT	10345-10364	VP24	AUGGCUAAAGCUACGGGACG	10345-10364	95	100	98.4	16
EBOLAID055 Raw data Min-max	PCR primer forward	ZEBOV-F	TGGAAAAAACATTAAGAGAACACTTGC	847-873	NP	UGGAAAAAACAUUAAGAGAACACUUGC	847-873	92.59	100	97.62	17
EBOLAID056 Raw data Min-max	PCR primer reverse	ZEBOV-R	AGGAGAGAAACTGACCGGCAT	906-926	NP	AUGCCGGUCAGUUUCUCUCCU	906-926	85.71	100	97.6	17
EBOLAID057 Raw data Min-max	Probe (FAM & BlackHole Quenche(...)	ZEBOV-P	CATGCCGGAAGAGGAGACAACTGAAGC	877-903	NP	CAUGCCGGAAGAGGAGACAACUGAAGC	877-903	96.3	100	99.33	17
EBOLAID058 Raw data Min-max	PCR primer forward	rt_EBOV-f	ATTTGAATGGGGTCCAATTGCC	13997-14018	L	AUUUGAAUGGGGUCCAAUUGCC	13997-14018	100	100	100	22
EBOLAID059 Raw data Min-max	PCR primer reverse	rt_EBOL-r	AAGCAGTRCCTATACTAGCCA	14090-14110	L	UGGCUAGUAUAGGCACUGCUU	14090-14110	85.71	80	97.57	22
EBOLAID060 Raw data Min-max	Probe (Taqman)	EBOV_prb	AGTCCCTTAAAACGGCTACAAGAATGGGAC	14021-14050	L	AGUCCCUUAAAACGGCUACAAGAAUGGCAC	14021-14047	100	100	100	22
EBOLAID061 Raw data Min-max	Primer forward	F3	GACGGGAGTGAGTGTCTACC	6387-6406	GP	GACGGGAGUGAGUGUCUACC	6387-6406	100	100	100	23
EBOLAID062 Raw data Min-max	Primer reverse	B3	AGCTTGGGGCAGTATCAGAA	6586-6605	GP	UUCUGAUACUGCCCCAAGCU	6586-6605	100	100	100	23
EBOLAID063 Raw data Min-max	Primer reverse	FL	GCACATACCGGCACC	6439-6453	GP	GGUGCCGGUAUGUGC	6439-6453	100	100	100	23
EBOLAID064 Raw data Min-max	Primer forward	BL	CTTCCTGTATGATCGACTTGCTTC	6515-6538	GP	CUUCCUGUAUGAUCGACUUGCUUC	6515-6538	95.83	100	99.68	23
EBOLAID065 Raw data Min-max	Primer forward	F3	CAATAAACAACTATTTAAATAAC	18321-18343	3'UTR	CAAUAAACAACUAUUUAAAUAAC	18321-18343	86.96	80	97.74	24
EBOLAID066 Raw data Min-max	Primer reverse	B3	CTGGCAAGATATTGATACAACA	18530-18551	3'UTR	UGUUGUAUCAAUAUCCUGUCAG	18530-18544	86.67	80	98.62	24
EBOLAID067 Raw data Min-max	Primer reverse	LF	AATTTTTTGATTATCACGC	18388-18406	3'UTR	GCGUGAUAAUCAAAAAAUU	18388-18406	94.74	80	99.69	24
EBOLAID068 Raw data Min-max	Primer forward	F3	TGAAGTCAAGAAGCGTGATGG	787-807	NP	UGAAGUCAAGAAGCGUGAUGG	787-807	90.48	100	97.94	24
EBOLAID069 Raw data Min-max	Primer reverse	B3	AGTCCTTGCTCTGCATGTACT	1000-1020	NP	AGUACAUGCAGAGCAAGGACU	1000-1020	100	100	100	24
EBOLAID070 Raw data Min-max	Primer reverse	LF	TGTTTTTTCCACTAGATACTGCTGG	833-857	NP	CCAGCAGUAUCUAGUGGAAAAAACA	833-857	92	100	97.43	24
EBOLAID071 Raw data Min-max	Primer forward	LB	TCCTTCCGAAATTGGTAGTAGGA	939-961	NP	UCCUUCCGAAAUUGGUAGUAGGA	939-961	100	100	100	24
EBOLAID072 Raw data Min-max	Primer forward	EBOV-F3	TGGTTCAAGTGCACAGTCAA	7086-7105	GP	UGGUUCAAGUGCACAGUCAA	7086-7105	95	80	99.9	25
EBOLAID073 Raw data Min-max	Primer reverse	EBOV-B3	TGTCTGCTCTACGGTGATGT	7255-7274	GP	ACAUCACCGCAGAACAGACA	7255-7274	85	100	96.69	25
EBOLAID074 Raw data Min-max	Primer reverse	EBOV-LF	GCAAGGGTTGTCAGATGCG	7125-7143	GP	CGCAUCUAACAACCCUUGC	7125-7143	84.21	100	99.49	25
EBOLAID075 Raw data Min-max	Primer forward	EBOV-LB	ATAATACACCCGTGTATAAACTTGAC	7203-7228	GP	AUAAUACACCCGUGUAUAAACUUGAC	7203-7228	92.31	100	98.87	25
EBOLAID076 Raw data Min-max	PCR primer forward	ZEBOV Forward	CGAACTTGACCATCTTGGACTTG	1552-1574	NP	CGAACUUGACCAUCUUGGACUUG	1552-1574	95.65	100	98.61	26
EBOLAID077 Raw data Min-max	PCR primer reverse	ZEBOV Reverse	TCCTCGTCGTCCTCGTCTAGAT	1929-1950	NP	AUCUAGACGAGGACGACGAGGA	1929-1950	95.45	100	99.41	26
EBOLAID078 Raw data Min-max	Primer forward	EBO-RPA-F	TAGTAGGAGAAAAGGCTTGCCTTGAGAAGG(...)	954-983	NP	UAGUAGGAGAAAAGGCUUGCCUUGAGAAGG	954-983	93.33	80	99.68	27
EBOLAID079 Raw data Min-max	Primer reverse	EBO-RPA-R	TGTTCGCATCAAACGGAAAATCACCATCAT(...)	1057-1087	NP	CAUGAUGGUGAUUUUCCGUUUGAUGCGAAC(...)	1057-1087	100	100	100	27
EBOLAID080 Raw data Min-max	Probe	EBO-RPA-P	TCAAGTACATGCAGAGCAAGGACTGATACA(...)	997-1028	NP	UCAAGUACAUGCAGAGCAAGGACUGAUACA(...)	997-1028	96.88	80	99.88	27