Search for the best oligonucleotides according to the degree of conservation in Marburg sequence alignments

The table describes for each oligonucleotide different measures of sequence conservation:
-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.

Database reference	Target	Original name	Sequence (5-3)	Position in reference genome	Genomic region	Sequence in reference genome	Position in Marburg_alig01	PIS	3'PIS	PPI	Related publication
Database reference	Target	Original name	Sequence (5-3)	Position in reference genome	Genomic region	Sequence in reference genome	Position in Marburg_alig01	PIS	3'PIS	PPI	Related publication
EBOLAID001	PCR primer forward	EBO-1	TGGGTAATYATCCTYTTCCA	5962-5981	GP	ATCAGTCTTATCTTAATTCA	6682-6701	35	60	91.32	1
EBOLAID002	PCR primer reverse	EBO-2	ACGACACCTTCAGCRAAAGT	6415-6434	GP	GTCTTCACTGAAGGGAACAT	7146-7165	55	40	95.81	1
EBOLAID003	PCR primer forward	EBO-3	GTTTGTCGKGACAAACTGTC	6041-6060	GP	ATTCGGTATGCTCCGGAACT	6772-6791	20	0	91.81	1
EBOLAID004	PCR primer reverse	EBO-4	TGGAARGCWAAGTCWCCGG	6335-6353	GP	CACAGGGGATCGCCCTTCA	7066-7084	42.11	20	90.69	1
EBOLAID005	PCR primer forward	GAB-1	GAATGTAGGTAGAACCTTCGG	13160-13180	L	GAATATAGGAAGAACTTTTGG	14170-14190	66.67	80	91.9	1
EBOLAID006	PCR primer reverse	GAB-2	GCATATAACACTGTGGGATTG	13492-13512	L	TAATACCACTATGTTATATGC	14502-14522	71.43	60	96.98	1
EBOLAID007	PCR primer forward	EBO-BP1	AATGGGCTGAAAATTGCTACAATC	6200-6223	GP	AGGAAGCCAAAACATGCTACAATA	6931-6954	54.17	80	94.75	2
EBOLAID008	PCR primer reverse	EBO-GP2	TTTTTTTAGTTTCCCAGAAGGCCCACT	6752-6771	GP	CAGGGTCCGGAGAACGAGAA	7512-7535	29.17	20	86.23	2
EBOLAID009	PCR primer forward	ZAI-NP1	GGACCGCCAAGGTAAAAAATGA	855-876	NP	GGACCTCCAAAGTAAAAAATGA	1282-1303	68.18	80	95.9	2
EBOLAID010	PCR primer reverse	ZAI-NP2	GCATATTGTTGGAGTTGCTTCTCAGC	1097-1122	NP	GCGGAAGTAAAACTACAAAGGCGACA	1524-1549	38.46	80	92.13	2
EBOLAID011	PCR primer forward		ATCGGAATTTTCTTTCTCATTGAAAGA	13123-13150	L	ATAGGAATTTTTCCTTCTCATTAAAAGA	14133-14160	75	80	94.15	3; 4;
EBOLAID012	PCR primer reverse		ATGTGGTGGATTATAATAATCACTGACATG(...)	13509-13541	L	ATGCATGTCAGTGACTTTTATAGCCCACCA(...)	14519-14551	78.79	100	95.67	3; 4;
EBOLAID013	PCR primer forward	EBOGP-1Df	TGGGCTGAAAAYTGCTACAATC	6202-6223	GP	GAAGCCAAAACATGCTACAATA	6933-6954	54.55	80	95.84	5
EBOLAID014	PCR primer reverse	EBOGP-1Dr	CTTTGTGMACATASCGGCAC	6294-6313	GP	ATGCAAAACTATCCATCATA	7025-7044	35	40	91.47	5
EBOLAID015	Probe	EBOGP-1DZPrb	CTACCAGCAGCGCCAGACGG	6256-6275	GP	CTGTTAGATCCTCCTACCAA	6987-7006	30	0	89.42	5
EBOLAID016	PCR primer forward	FILO-A	ATCGGAATTTTTCTTTCTCATT	13123-13144	L	ATAGGAATTTTTCCTTCTCATT	14133-14154	77.27	100	94.11	2; 1; 5; 6;
EBOLAID017	PCR primer reverse	FILO-B	ATGTGGTGGGTTATAATAATCACTGACATG	13512-13541	L	CATGTCAGTGACTTTTATAGCCCACCACAT	14522-14551	76.67	100	95.24	2; 1; 5; 6; 7;
EBOLAID018	PCR primer forward	EBOORF UP	ATGGATTCTCGTCCTCAGAAAAT	52-74	NP	GAATATTAACATTGACATTGAGA	470-492	34.78	20	97.04	8
EBOLAID019	PCR primer reverse	EBOORF DP	TCACTGATGATGTTGCAGGATT	2271-2281	NP	AATATTTGAAC	2747-2757	45.45	60	87.09	8
EBOLAID020	PCR primer forward	ENZ FP	ATGATGGAAGCTACGGCG	1437-1447	NP	AATCTACAGAA	1868-1885	27.78	20	82.12	8
EBOLAID021	PCR primer reverse	ENZ RP	AGGACCAAGTCATCTGGTGC	1475-1488	NP	GACTTGAATGATCC	1918-1937	30	20	93.62	8
EBOLAID022	Probe	ENZ P	CCAGAGTTACTCGGAAAACGGCATG	1452-1471	NP	GCTCTTCTTCAAGTAGCTTT	1890-1914	32	40	92.75	8
EBOLAID023	PCR primer forward	SudZaiNP1(+)	GAGACAACGGAAGCTAATGC	470-489	NP	GAATCTCAGAGGGGGAGAAT	897-916	25	20	94.54	9
EBOLAID024	PCR primer reverse	SudZaiNP1(-)	AACGGAAGATCACCATCATG	637-656	NP	CATGAAAGTAATTTTCGGGA	1064-1083	55	80	91.56	9
EBOLAID025	PCR primer forward	SudZaiNP2(+)	GGTCAGTTTCTATCCTTTGC	491-510	NP	GGGCTCTTTTTATCATTTTG	918-937	50	40	93.08	9
EBOLAID026	PCR primer reverse	SudZaiNP2(-)	CATGTGTCCAACTGATTGCC	621-640	NP	GGCTTACCACAGGCCACATG	1048-1067	60	60	92.21	9
EBOLAID027	PCR primer forward	EBsp5	TTYCCTAGCAAYATGATGG	13254-13272	L	TTCCCTAGTAACATGATGG	14264-14282	78.95	100	95.58	10; 4;
EBOLAID028	PCR primer reverse	EBsp3	TATAATAATCACTGACATGCAT	13509-13530	L	ATGCATGTCAGTGACTTTTATA	14519-14540	90.91	100	98.06	10; 4;
EBOLAID029	PCR primer forward	evR3	TCTTGCAAGGACCGCCAAGGTAAAAA	847-872	NP	TTTGGTGCGGACCTCCAAAGTAAAAA	1274-1299	53.85	80	93.35	11
EBOLAID030	PCR primer reverse	evF3	TTCAAAAGTCGGGCGAAAGGAGCATA	926-951	NP	TACGCACCATTTGCACGGGTTCTGAA	1353-1378	65.38	80	95.1	11
EBOLAID031	PCR primer forward	F3	AATAACGAAAGGAGTCCCTA	18572-18590	3'UTR	AATAAGAAAACGAAAAGA-C	19662-19681	30	0	78.43	12
EBOLAID032	PCR primer reverse	B3	TTGTATCAATATCCTGTCAG	18775-18793	3'UTR	CTTGAGCTTTATCCC-TAAT	19871-19890	30	40	84.08	12
EBOLAID033	PCR primer forward	Ebola-1F	GATGCAGTATTCGAGCCTAATGTTCTAG	12972-12999	L	GACAGTGTCTTCGATAGAAGTGTATTAG	13982-14009	53.57	60	91.47	13
EBOLAID034	PCR primer reverse	Ebola-1R	GTGTTTGAACATTGCGAGTCGGATAAG	13189-13215	L	CGTATCGTGTCAGAAATGTCCAAACAC	14199-14225	66.67	80	97.31	13
EBOLAID035	Probe	Ebola-P	ACTCGAGTATCTACTACCACAATATCGGAA(...)	13100-13130	L	GTTAGAGTATTTGGCTCCTTCTTATAGGAA(...)	14110-14140	48.39	60	92.06	13
EBOLAID036	PCR primer forward	FiloA2.4	AAGCATTTCCTAGCAATATGATGGT	13249-13273	L	AAGCATTCCCTAGTAACATGATGGT	14259-14283	80	100	95.37	7
EBOLAID037	PCR primer forward	FiloA2.2	AAGCCTTTCCTAGCAACATGATGGT	13249-13273	L	AAGCATTCCCTAGTAACATGATGGT	14259-14283	80	100	95.37	7
EBOLAID038	PCR primer forward	FiloA2.3	AAGCATTCCCTAGCAACATGATGGT	13249-13273	L	AAGCATTCCCTAGTAACATGATGGT	14259-14283	80	100	95.37	7
EBOLAID039	PCR primer reverse	FILO B-Ra	GTGAGGAGGGCTATAAAAGTCACTGACATG	13512-13530	L	CATGTCAGTGACTTTTATA	14522-14540	89.47	100	97.75	7
EBOLAID040	Probe (FAM & BlackHole Quenche(...)	FAMEBOSu	CCGAAATCATCACTIGTITGGTGCCA	13320-13342	L	TGGCACCACAATTCAGCAAGCAT	14330-14352	47.83	20	95.32	7
EBOLAID041	Probe (FAM & BlackHole Quenche(...)	FAMEBOg	CCAAAATCATCACTIGTGTGGTGCCA	13320-13345	L	TGGCACCACAATTCAGCAAGCATAGG	14330-14355	50	60	95.77	7
EBOLAID042	Probe (FAM & BlackHole Quenche(...)	FAMMBG	CCTATGCTTGCTGAATTGTGGTGCCA	13320-13329	L	TGGCACCACA	14330-14339	90	80	95.58	7
EBOLAID043	PCR primer forward	F565	TCTGACATGGATTACCACAAGATC	101-121	NP	GAGATGGATTTACACAGTTTG	519-542	45.83	20	92.67	14
EBOLAID044	PCR primer reverse	R640	GGATGACTCTTTGCCGAACAATC	154-173	NP	TGTTCGTAATAAGAAAGTGA	578-600	30.43	40	97.54	14
EBOLAID045	Probe (FAM&MGB)	p597S	AGGTCTGTCCGTTCAA	140-151	NP	CCCACTGCCCCT	561-572	33.33	20	89.74	14
EBOLAID046	PCR primer forward	F2000	TTTTCAATCCTCAACCGTAAGGC	7687-7709	GP	TTCTCCTTAATCAATAGACATGC	8466-8488	52.17	60	94.51	14
EBOLAID047	PCR primer reverse	R2079	CAGTCCGGTCCCAGAATGTG	7747-7766	GP	AAAGTGCTTGGACCTGATTG	8526-8545	65	40	95.77	14
EBOLAID048	Probe (FAM&TAMRA)	p2058A	CATGTGCCGCCCCATCGCTGC	7725-7745	GP	CACAAGATGGGGAGGAACATG	8504-8524	61.9	100	92.94	14
EBOLAID049	PCR primer forward	PanFilo-L1	ATMGRAAYTTTTCYTTYTCWYT	13123-13141	L	ATAGGAATTTTTCCTTCTC	14133-14151	73.68	80	93.18	15
EBOLAID050	PCR primer reverse	Panfilo-L2	TGWGGHGGRYTATAAWARTCACTDACAT	13513-13540	L	ATGTCAGTGACTTTTATAGCCCACCACA	14523-14550	78.57	100	96.04	15
EBOLAID051	PCR primer forward	PanFilo-L3	GCNAARGCMTTYCCHAGYAAYATGATGG	13248-13272	L	AAAGCATTCCCTAGTAACATGATGG	14258-14282	80	100	95.37	15
EBOLAID052	PCR primer reverse	Panfilo-L4	ATAAWARTCACTDACATGCATRTARCA	13503-13529	L	TGTTATATGCATGTCAGTGACTTTTAT	14513-14539	85.19	80	96.41	15
EBOLAID053	PCR primer forward (confirmar)	KGH-F	GTCGTTCCAACAATCGAGCG	10084-10103	VP24	ACCAGATCACGGATCAAGCA	11041-11060	25	20	81.51	16
EBOLAID054	PCR primer forward (confirmar)	KGH-R	CGTCCCGTAGCTTTRGCCAT	10207-10226	VP24	ATGGCAGAATTATCAACGCG	11167-11186	50	40	93.5	16
EBOLAID055	PCR primer forward	ZEBOV-F	TGGAAAAAACATTAAGAGAACACTTGC	427-453	NP	TTACAGCCCTTTAATTCTAGCCCTTAA	854-880	25.93	40	89.69	17
EBOLAID056	PCR primer reverse	ZEBOV-R	AGGAGAGAAACTGACCGGCAT	486-506	NP	GAATTGGGCTCTTTTTATCAT	913-933	42.86	0	92.08	17
EBOLAID057	Probe (FAM & BlackHole Quenche(...)	ZEBOV-P	CATGCCGGAAGAGGAGACAACTGAAGC	457-483	NP	ATTGGAAAGTACTGAATCTCAGAGGGG	884-910	18.52	20	92.97	17