Find PCR primer pairs ordered by the average degree of conservation in diverse sequence alignments

The table lists different measures of sequence conservation for all pairs of PCR primers with a predicted amplicon >70 bp and <1000 bp in the HIV reference genome:
-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
-HIVoligoDB score: mean value of PIS, 3'PIS and PPI
-Melting temperature (Tm)
-Free energy is presented in kcal/mol. Formation of dimers is more probable if the free energy is very low (<-7 kcal/mol).
The mean values for each oligonucleotide were obtained considering all sequence alignments used the database. The mean value of both primers for each pair is indicated in the table.

Primer 1	Primer 2	Amplicon length	Mean PIS	Mean 3'PIS	Mean PPI	Score	Primer 1 Tm	Primer 2 Tm	Dimer Free Energy
Primer 1	Primer 2	Amplicon length	Mean PIS	Mean 3'PIS	Mean PPI	Score	Primer 1 Tm	Primer 2 Tm	Dimer Free Energy
HIV2ID0001	HIV2ID0002	391	43.82	30	92.69	55.5	61.25	60.98	-4.1
HIV2ID0001	HIV2ID0007	521	56.82	50	93.13	66.65	61.25	60.11	-7.2
HIV2ID0001	HIV2ID0026	101	44.32	30	92.52	55.61	61.25	57.37	-8.6
HIV2ID0001	HIV2ID0029	608	66.03	60	91.64	72.56	61.25	53.33	-4.5
HIV2ID0001	HIV2ID0035	732	63.07	50	89.53	67.53	61.25	58.93	-6.1
HIV2ID0001	HIV2ID0052	544	60.98	50	92.5	67.83	61.25	59.05	-6.5
HIV2ID0001	HIV2ID0064	479	50.57	30	96.31	58.96	61.25	60.96	-5.4
HIV2ID0002	HIV2ID0008	578	37	20	88.89	48.63	60.98	60.50	-10.1
HIV2ID0002	HIV2ID0025	510	24.5	30	91.8	48.77	60.98	56.86	-8.1
HIV2ID0002	HIV2ID0028	193	38.31	30	88.24	52.19	60.98	57.06	-7.9
HIV2ID0002	HIV2ID0032	681	12	10	86.22	36.07	60.98	59.11	-4.5
HIV2ID0002	HIV2ID0036	812	34.73	30	93.81	52.84	60.98	57.25	-6.3
HIV2ID0002	HIV2ID0039	177	42	40	89.66	57.22	60.98	55.00	-5.9
HIV2ID0002	HIV2ID0051	347	43.25	30	92.87	55.37	60.98	63.24	-4.1
HIV2ID0002	HIV2ID0053	174	39.09	40	91.25	56.78	60.98	58.28	-5.9
HIV2ID0003	HIV2ID0004	105	57.51	60	93.1	70.2	57.63	60.11	-6.8
HIV2ID0003	HIV2ID0011	754	48.42	40	88	58.8	57.63	57.72	-6.4
HIV2ID0003	HIV2ID0041	905	69.78	80	92.85	80.88	57.63	49.21	-5
HIV2ID0003	HIV2ID0043	540	69.78	80	91.79	80.52	57.63	53.36	-7
HIV2ID0003	HIV2ID0047	575	51.45	60	89.53	66.99	57.63	67.13	-6.3
HIV2ID0003	HIV2ID0048	711	53.53	90	84.67	76.07	57.63	60.83	-5.6
HIV2ID0004	HIV2ID0038	339	48.65	30	93.01	57.22	60.11	64.79	-5.2
HIV2ID0004	HIV2ID0044	787	55.08	70	90.08	71.72	60.11	51.76	-8
HIV2ID0004	HIV2ID0046	229	45.45	60	93.72	66.39	60.11	68.14	-7.6
HIV2ID0006	HIV2ID0007	152	38.63	50	91.62	60.08	57.28	60.11	-5.5
HIV2ID0006	HIV2ID0009	692	40.91	50	89.21	60.04	57.28	59.92	-5.4
HIV2ID0006	HIV2ID0026	470	26.13	30	91	49.04	57.28	57.37	-8.5
HIV2ID0006	HIV2ID0029	239	47.84	60	90.12	65.99	57.28	53.33	-6.7
HIV2ID0006	HIV2ID0033	349	44.59	50	93.34	62.64	57.28	58.57	-3.2
HIV2ID0006	HIV2ID0035	363	44.88	50	88.02	60.97	57.28	58.93	-8.9
HIV2ID0006	HIV2ID0050	349	44.88	60	93.64	66.17	57.28	63.24	-3.2
HIV2ID0006	HIV2ID0052	175	42.8	50	90.97	61.26	57.28	59.05	-3.7
HIV2ID0006	HIV2ID0064	848	32.38	30	94.8	52.39	57.28	60.96	-8.7
HIV2ID0007	HIV2ID0008	443	50	40	89.33	59.77	60.11	60.50	-10.5
HIV2ID0007	HIV2ID0025	645	37.5	50	92.23	59.91	60.11	56.86	-7.5
HIV2ID0007	HIV2ID0032	816	25	30	86.66	47.22	60.11	59.11	-6.4
HIV2ID0007	HIV2ID0034	144	25	30	85.95	46.98	60.11	47.59	-6.5
HIV2ID0007	HIV2ID0036	947	47.73	50	94.25	63.99	60.11	57.25	-4.6
HIV2ID0007	HIV2ID0051	482	56.25	50	93.31	66.52	60.11	63.24	-7.2
HIV2ID0008	HIV2ID0009	137	52.27	40	86.92	59.73	60.50	59.92	-4.6
HIV2ID0008	HIV2ID0018	871	57.69	50	88.13	65.27	60.50	57.42	-6.6
HIV2ID0008	HIV2ID0029	316	59.21	50	87.83	65.68	60.50	53.33	-8
HIV2ID0008	HIV2ID0033	904	55.95	40	91.06	62.34	60.50	58.57	-7.8
HIV2ID0008	HIV2ID0035	192	56.25	40	85.72	60.66	60.50	58.93	-8.2
HIV2ID0008	HIV2ID0050	904	56.25	50	91.35	65.87	60.50	63.24	-7.8
HIV2ID0008	HIV2ID0052	380	54.16	40	88.69	60.95	60.50	59.05	-4
HIV2ID0008	HIV2ID0054	864	57.5	50	87.81	65.1	60.50	55.57	-6.6
HIV2ID0009	HIV2ID0017	528	63.81	70	91.06	74.96	59.92	55.47	-4
HIV2ID0009	HIV2ID0021	618	51.27	50	86.89	62.72	59.92	53.36	-4.7
HIV2ID0009	HIV2ID0028	480	53.59	50	86.28	63.29	59.92	57.06	-8.2
HIV2ID0009	HIV2ID0034	682	27.27	30	83.55	46.94	59.92	47.59	-6.5
HIV2ID0009	HIV2ID0039	496	57.27	60	87.69	68.32	59.92	55.00	-4.8
HIV2ID0009	HIV2ID0053	499	54.36	60	89.29	67.88	59.92	58.28	-4.4
HIV2ID0009	HIV2ID0055	521	67.75	60	92.89	73.55	59.92	50.44	-3.3
HIV2ID0010	HIV2ID0011	310	37.55	20	89.19	48.91	56.88	57.72	-7.7
HIV2ID0010	HIV2ID0045	994	53.91	40	92.8	62.24	56.88	51.00	-2.6
HIV2ID0010	HIV2ID0047	489	40.58	40	90.72	57.1	56.88	67.13	-13.4
HIV2ID0010	HIV2ID0048	353	42.66	70	85.87	66.18	56.88	60.83	-2.6
HIV2ID0010	HIV2ID0065	659	51.41	20	95.69	55.7	56.88	54.44	-5.8
HIV2ID0011	HIV2ID0038	311	39.56	10	87.91	45.82	57.72	64.79	-5
HIV2ID0011	HIV2ID0046	879	36.36	40	88.62	54.99	57.72	68.14	-6.5
HIV2ID0011	HIV2ID0049	851	30.3	30	83.29	47.86	57.72	67.98	-6.9
HIV2ID0012	HIV2ID0013	198	57.03	50	87.41	64.81	53.11	50.53	-6.4
HIV2ID0012	HIV2ID0015	146	73.8	80	93.09	82.3	53.11	49.40	-4.2
HIV2ID0012	HIV2ID0024	283	62.43	70	90.44	74.29	53.11	60.91	-3.9
HIV2ID0012	HIV2ID0056	952	52.61	60	88.25	66.95	53.11	60.46	-4.7
HIV2ID0012	HIV2ID0057	268	69.05	70	92.21	77.09	53.11	51.65	-2.7
HIV2ID0012	HIV2ID0060	337	65.73	70	89.69	75.14	53.11	58.80	-4.6
HIV2ID0013	HIV2ID0059	133	52.17	30	90.41	57.52	50.53	51.50	-5.2
HIV2ID0013	HIV2ID0061	161	60.87	70	90.61	73.83	50.53	58.80	-5.4
HIV2ID0014	HIV2ID0041	402	35	40	78.19	51.06	36.52	49.21	-2.3
HIV2ID0014	HIV2ID0043	767	35	40	77.13	50.71	36.52	53.36	-3.5
HIV2ID0014	HIV2ID0062	628	10	10	68.63	29.54	36.52	60.54	-2.5
HIV2ID0015	HIV2ID0059	83	68.94	60	96.09	75.01	49.40	51.50	-2
HIV2ID0015	HIV2ID0061	211	77.64	100	96.3	91.31	49.40	58.80	-4.4
HIV2ID0017	HIV2ID0018	252	69.23	80	92.28	80.5	55.47	57.42	-6.7
HIV2ID0017	HIV2ID0029	935	70.75	80	91.97	80.91	55.47	53.33	-6.3
HIV2ID0017	HIV2ID0035	811	67.79	70	89.87	75.89	55.47	58.93	-4.3
HIV2ID0017	HIV2ID0052	999	65.7	70	92.83	76.18	55.47	59.05	-4.8
HIV2ID0017	HIV2ID0054	245	69.04	80	91.95	80.33	55.47	55.57	-6.7
HIV2ID0018	HIV2ID0021	112	56.69	60	88.1	68.27	57.42	53.36	-6.1
HIV2ID0018	HIV2ID0055	209	73.16	70	94.1	79.09	57.42	50.44	-6.8
HIV2ID0018	HIV2ID0058	775	56.5	60	88.41	68.3	57.42	55.95	-4
HIV2ID0021	HIV2ID0035	902	55.25	50	85.7	63.65	53.36	58.93	-8.9
HIV2ID0021	HIV2ID0054	154	56.5	60	87.78	68.09	53.36	55.57	-6.1
HIV2ID0022	HIV2ID0024	179	61.78	70	94.3	75.36	58.73	60.91	-10.1
HIV2ID0022	HIV2ID0057	164	68.4	70	96.08	78.16	58.73	51.65	-9.5
HIV2ID0022	HIV2ID0060	233	65.09	70	93.56	76.22	58.73	58.80	-8.1
HIV2ID0024	HIV2ID0059	214	57.56	50	93.43	67	60.91	51.50	-6.2
HIV2ID0024	HIV2ID0061	80	66.27	90	93.63	83.3	60.91	58.80	-6.8
HIV2ID0025	HIV2ID0029	770	46.71	60	90.74	65.82	56.86	53.33	-4.6
HIV2ID0025	HIV2ID0033	182	43.45	50	93.97	62.47	56.86	58.57	-4.8
HIV2ID0025	HIV2ID0035	894	43.75	50	88.63	60.79	56.86	58.93	-6.1
HIV2ID0025	HIV2ID0050	182	43.75	60	94.26	66	56.86	63.24	-4.8
HIV2ID0025	HIV2ID0052	706	41.66	50	91.59	61.09	56.86	59.05	-8.4
HIV2ID0025	HIV2ID0064	317	31.25	30	95.41	52.22	56.86	60.96	-5.1
HIV2ID0026	HIV2ID0028	679	38.81	30	88.06	52.29	57.37	57.06	-7
HIV2ID0026	HIV2ID0032	195	12.5	10	86.05	36.18	57.37	59.11	-5.1
HIV2ID0026	HIV2ID0034	477	12.5	10	85.34	35.95	57.37	47.59	-5.8
HIV2ID0026	HIV2ID0036	326	35.23	30	93.63	52.95	57.37	57.25	-4.6
HIV2ID0026	HIV2ID0039	663	42.5	40	89.48	57.33	57.37	55.00	-6.6
HIV2ID0026	HIV2ID0051	139	43.75	30	92.69	55.48	57.37	63.24	-8.6
HIV2ID0026	HIV2ID0053	660	39.59	40	91.08	56.89	57.37	58.28	-6.4
HIV2ID0028	HIV2ID0033	522	57.27	50	90.41	65.89	57.06	58.57	-5.7
HIV2ID0028	HIV2ID0035	190	57.56	50	85.08	64.21	57.06	58.93	-6.1
HIV2ID0028	HIV2ID0050	522	57.56	60	90.7	69.42	57.06	63.24	-5.7
HIV2ID0029	HIV2ID0032	904	34.21	40	85.17	53.13	53.33	59.11	-4.5
HIV2ID0029	HIV2ID0034	232	34.21	40	84.46	52.89	53.33	47.59	-7.3
HIV2ID0029	HIV2ID0051	570	65.46	60	91.81	72.42	53.33	63.24	-4.5
HIV2ID0029	HIV2ID0055	971	74.69	70	93.8	79.5	53.33	50.44	-4.9
HIV2ID0032	HIV2ID0033	354	30.95	30	88.39	49.78	59.11	58.57	-4.1
HIV2ID0032	HIV2ID0050	354	31.25	40	88.69	53.31	59.11	63.24	-4.1
HIV2ID0032	HIV2ID0052	878	29.16	30	86.03	48.4	59.11	59.05	-7.4
HIV2ID0032	HIV2ID0064	145	18.75	10	89.84	39.53	59.11	60.96	-7.1
HIV2ID0033	HIV2ID0034	357	30.95	30	87.69	49.54	58.57	47.59	-7.9
HIV2ID0033	HIV2ID0036	446	53.67	50	95.97	66.55	58.57	57.25	-2.8
HIV2ID0033	HIV2ID0039	543	60.95	60	91.82	70.92	58.57	55.00	-4.6
HIV2ID0033	HIV2ID0053	540	58.03	60	93.42	70.49	58.57	58.28	-4.7
HIV2ID0034	HIV2ID0035	392	31.25	30	82.35	47.87	47.59	58.93	-5.6
HIV2ID0034	HIV2ID0050	320	31.25	40	87.98	53.08	47.59	63.24	-7.9
HIV2ID0034	HIV2ID0052	204	29.16	30	85.31	48.16	47.59	59.05	-6.1
HIV2ID0034	HIV2ID0064	819	18.75	10	89.13	39.29	47.59	60.96	-6.6
HIV2ID0035	HIV2ID0039	165	61.25	60	86.5	69.25	58.93	55.00	-6.9
HIV2ID0035	HIV2ID0051	689	62.5	50	89.7	67.4	58.93	63.24	-6.2
HIV2ID0035	HIV2ID0053	168	58.34	60	88.09	68.81	58.93	58.28	-8.1
HIV2ID0035	HIV2ID0055	852	71.72	60	91.69	74.47	58.93	50.44	-3.3
HIV2ID0036	HIV2ID0050	486	53.98	60	96.27	70.08	57.25	63.24	-2.8
HIV2ID0037	HIV2ID0038	644	54.87	30	93.84	59.57	59.33	64.79	-3
HIV2ID0037	HIV2ID0049	518	45.61	50	89.23	61.62	59.33	67.98	-10.6
HIV2ID0038	HIV2ID0043	936	60.92	50	91.7	67.54	64.79	53.36	-3.3
HIV2ID0038	HIV2ID0045	326	55.92	30	91.51	59.15	64.79	51.00	-2.7
HIV2ID0038	HIV2ID0047	179	42.59	30	89.44	54.01	64.79	67.13	-6.2
HIV2ID0038	HIV2ID0048	315	44.67	60	84.58	63.09	64.79	60.83	-3.2
HIV2ID0039	HIV2ID0050	505	61.25	70	92.12	74.46	55.00	63.24	-4.6
HIV2ID0040	HIV2ID0041	664	59	70	89.23	72.74	54.17	49.21	-4.2
HIV2ID0040	HIV2ID0062	366	34	40	79.67	51.22	54.17	60.54	-4.3
HIV2ID0041	HIV2ID0042	141	66.82	80	92.56	79.79	49.21	46.35	-5
HIV2ID0041	HIV2ID0044	220	67.35	90	89.83	82.39	49.21	51.76	-5.6
HIV2ID0041	HIV2ID0046	778	57.73	80	93.47	77.07	49.21	68.14	-7.3
HIV2ID0041	HIV2ID0063	542	57.91	60	92.59	70.17	49.21	57.00	-3.6
HIV2ID0042	HIV2ID0043	546	66.82	80	91.5	79.44	46.35	53.36	-3.4
HIV2ID0042	HIV2ID0062	849	41.82	50	83	58.27	46.35	60.54	-4
HIV2ID0043	HIV2ID0044	145	67.35	90	88.77	82.04	53.36	51.76	-4.6
HIV2ID0043	HIV2ID0046	413	57.73	80	92.41	76.71	53.36	68.14	-5.8
HIV2ID0043	HIV2ID0063	907	57.91	60	91.53	69.82	53.36	57.00	-8.1
HIV2ID0044	HIV2ID0045	790	62.35	70	88.58	73.64	51.76	51.00	-6.1
HIV2ID0045	HIV2ID0046	197	52.73	60	92.22	68.32	51.00	68.14	-6.9
HIV2ID0046	HIV2ID0047	753	39.39	60	90.15	63.18	68.14	67.13	-8.4
HIV2ID0046	HIV2ID0048	889	41.48	90	85.3	72.26	68.14	60.83	-6.2
HIV2ID0048	HIV2ID0049	896	35.41	80	79.97	65.13	60.83	67.98	-7.3
HIV2ID0049	HIV2ID0065	160	44.16	30	89.79	54.65	67.98	54.44	-6.5
HIV2ID0050	HIV2ID0053	543	58.34	70	93.72	74.02	63.24	58.28	-4.7
HIV2ID0051	HIV2ID0052	546	60.41	50	92.66	67.69	63.24	59.05	-6.5
HIV2ID0051	HIV2ID0064	477	50	30	96.48	58.83	63.24	60.96	-5.4
HIV2ID0053	HIV2ID0064	997	45.84	40	94.88	60.24	58.28	60.96	-7.9
HIV2ID0054	HIV2ID0055	208	72.97	70	93.78	78.92	55.57	50.44	-8.2
HIV2ID0054	HIV2ID0058	776	56.31	60	88.09	68.13	55.57	55.95	-4
HIV2ID0056	HIV2ID0058	414	45.47	50	88.97	61.48	60.46	55.95	-5.4
HIV2ID0057	HIV2ID0059	205	64.18	50	95.21	69.8	51.65	51.50	-5.5
HIV2ID0057	HIV2ID0061	89	72.88	90	95.41	86.1	51.65	58.80	-6.2
HIV2ID0059	HIV2ID0060	316	60.87	50	92.69	67.85	51.50	58.80	-7.7
HIV2ID0062	HIV2ID0063	488	32.91	30	83.03	48.65	60.54	57.00	-4.2