TABLE 1.

Sequences and relative fluorescence intensities of a set of oligonucleotide probes targeting the 23S ribosomal RNA of E. coli K-12

Probe name	E. coli position (5′→3′)a	Probe sequence (5′→3′)	Relative probe fluorescence (%)b	Brightness class
23S-1	1–18	ACGCTTAGTCGCTTAACC	34	IV
23S-19	19–36	CCAGGGCATCCACCGTGT	55	III
23S-37	37–54	CTTCATCGCCTCTGACTG	61	II
23S-55	55–72	ATCGCAGATTAGCACGTC	51	III
23S-73	73–90	ATCACCTCACCGACGCTT	52	III
23S-91	91–108	CCGGTTATAACGGTTCAT	27	IV
23S-109	109–126	TTCCCCATTCGGAAATCG	38	IV
23S-127	127–144	TGTCGAAACACACTGGGT	46	III
23S-145	145–163	GATTCAGTTAATGATAGTG	3	VI
23S-164	164–181	TCGCCTCATTAACCTATG	58	III
23S-182	182–199	TGTTTCAGTTCCCCCGGT	69	II
23S-200	200–217	TTCCTCGGGGTACTTAGA	33	IV
23S-218	218–235	AATCTCGGTTGATTTCTT	81	I
23S-236	236–252	CTCGCCGCTACTGGGGG	72	II
23S-253	253–269	GGGCTCCTCCCCGTTCG	57	III
23S-270	270–287	CACACTGATTCAGGCTCT	48	III
23S-288	288–305	GACGCTTCCACTAACACA	14	V
23S-306	306–323	GTATCGCGCGCCTTTCCA	61	II
23S-324	324–341	GTACGGGGCTGTCACCCT	63	II
23S-342	342–360	ACAATATGTGCATTTTTGT	13	V
23S-361	361–378	GCCCTACTCATCGAGCTC	68	II
23S-369	369–386	CGTGTCCCGCCCTACTCA	72	II
23S-387	387–404	TATTCAGACAGGATACCA	22	IV
23S-397	397–414	GGTCCCCCCATATTCAGA	74	II
23S-415	415–432	TATTTAGCCTTGGAGGAT	69	II
23S-433	433–450	CTATCGGTCAGTCAGGAG	67	II
23S-451	451–468	CCTCACGGTACTGGTTCA	66	II
23S-469	469–486	GGGTTCTTTTCGCCTTTC	77	II
23S-487	487–504	TTTTCACTCCCCTCGCCG	58	III
23S-505	505–522	TACACGGTTTCAGGTTCT	32	IV
23S-523	523–540	GCTCCCACTGCTTGTACG	79	II
23S-529	529–546	AAAGAGGCTCCCACTGCT	66	II
23S-547	547–564	GTACGCAGTCACCCCCAT	45	III
23S-560	560–577	CATTATACAAAAGGTACG	31	IV
23S-578	578–595	GAATATAAGTCGCTGACC	11	V
23S-596	596–613	TCGGTTAACCTTGCTACA	29	IV
23S-614	614–631	TCCCTTCGGCTCCCCTAT	66	II
23S-632	632–649	CCCAGTTAAGACTCGGTT	36	IV
23S-650	650–667	ATACCCTGCAACTTAACG	23	IV
23S-668	668–685	TCACCGGGTTTCGGGTCT	53	III
23S-686	686–703	AACCTGCCCATGGCTAGA	32	IV
23S-704	704–721	TAGTGTTACCCAACCTTC	23	IV
23S-722	722–739	TCGGTTCGGTCCTCCAGT	54	III
23S-731	731–748	CAACATTAGTCGGTTCGG	3	VI
23S-749	749–766	AGTCATCCGCTAATTTTT	14	V
23S-759	759–776	CCCAGCCACAAGTCATCC	48	III
23S-777	777–794	TTTGATTGGCCTTTCACC	58	III
23S-795	795–812	GAACCAGCTATCTCCCGG	61	II
23S-813	813–830	CTAAATAGCTTTCGGGGA	43	III
23S-831	831–848	GAATTCACGAGGCGCTAC	38	IV
23S-849	849–866	TGCTCTACCCCCGGAGAT	37	IV
23S-867	867–884	ACCCCCTTGCCGAAACAG	39	IV
23S-885	885–902	GGTTGGTAAGTCGGGATG	6	V
23S-903	903–920	TATTCGCAGTTTGCATCG	10	V
23S-921	921–938	CGTGATAACATTCTCCGG	3	VI
23S-930	930–947	TGTGTCTCCCGTGATAAC	37	IV
23S-939	939–955	ACCCGCCGTGTGTCTCC	49	III
23S-948	948–964	GACGTTAGCACCCGCCG	14	V
23S-956	956–973	TTCACGACGGACGTTAGC	4	VI
23S-965	965–982	GTTTCCCTCTTCACGACG	51	III
23S-974	974–991	GTCTGGGTTGTTTCCCTC	94	I
23S-992	992–1009	TTGGGACCTTAGCTGGCG	62	II
23S-1010	1010–1027	TCCCACTTAACCATGACT	56	III
23S-1028	1028–1045	GGGCCTTCCCACATCGTT	62	II
23S-1046	1046–1063	CCAACATCCTGGCTGTCT	53	III
23S-1064	1064–1081	ATGATGGCTGCTTCTAAG	42	III
23S-1082	1082–1100	GCTATTACGCTTTCTTTAA	42	III
23S-1101	1118–1118	GGCCGACTCGACCAGTGA	65	II
23S-1137	1137–1154	CGGTGCATGGTTTAGCCC	59	III
23S-1155	1155–1172	GTGTCGCTGCCGCAGCTT	60	III
23S-1173	1173–1191	CCTACCCAACAACACATA	58	III
23S-1192	1192–1209	AGGCTTACAGAACGCTCC	49	III
23S-1210	1210–1227	CTCACAGGCCACCTTCAC	61	II
23S-1228	1228–1245	CTGATACCTCCAGCAACC	32	IV
23S-1246	1246–1263	ATGTCAGCATTCGCACTT	61	II
23S-1264	1264–1281	CCCGCTTTATCGTTACTT	66	II
23S-1282	1282–1299	CGGCGAGCGGGCTTTTCA	42	III
23S-1300	1300–1317	CAGGAACCCTTGGTCTTC	66	II
23S-1310	1310–1327	TAACGTTGGACAGGAACC	44	III
23S-1328	1328–1345	GACTCACCCTGCCCCGAT	68	II
23S-1336	1336–1353	TAGGGGTCGACTCACCCT	63	II
23S-1354	1354–1370	GCCTTTCGGCCTCGCCT	52	III
23S-1371	1371–1388	CTGTTTCCCATCGACTAC	59	III
23S-1389	1389–1407	CAAGTACAGGAATATTAAC	3	VI
23S-1408	1408–1425	CCCCCTTCGCAGTAACAC	64	II
23S-1426	1426–1443	AACATAGCCTTCTCCGTC	74	II
23S-1444	1444–1460	ACAACCGTCGCCCGGCC	31	IV
23S-1461	1461–1478	CTACACGCTTAAACCGGG	6	V
23S-1467	1467–1484	ACCAGCCTACACGCTTAA	7	V
23S-1479	1479–1496	TTTGCCTGGAAAACCAGC	1	VI
23S-1485	1485–1502	TCCGGATTTGCCTGGAAA	7	V
23S-1491	1491–1508	TGGTTTTCCGGATTTGCC	9	V
23S-1497	1497–1514	CAGCCTTGGTTTTCCGGA	83	I
23S-1509	1509–1526	GTCATCACGCCTCAGCCT	45	III
23S-1515	1515–1532	TGCCTCGTCATCACGCCT	56	III
23S-1524	1524–1541	GCACCGTAGTGCCTCGTC	6	V
23S-1533	1533–1551	TGTCGCTTCAGCACCGTAG	15	V
23S-1552	1552–1569	TCCTGGAAGCAGGGCATT	24	IV
23S-1570	1570–1587	CTGATGCTTAGAGGCTTT	10	V
23S-1588	1588–1605	GGTACGATTTGATGTTAC	6	V
23S-1606	1606–1623	CCACCTGTGTCGGTTTGG	64	II
23S-1615	1615–1632	TCTACCTGACCACCTGTG	58	III
23S-1633	1633–1650	TCAAGCGCCTTGGTATTC	65	II
23S-1642	1642–1659	CGAGTTCTCTCAAGCGCC	62	II
23S-1660	1660–1677	TTGCCTAGTTCCTTCACC	57	III
23S-1678	1678–1695	CGAAGTTACGGCACCATT	41	III
23S-1696	1696–1713	TATCAGCGTGCCTTCTCC	94	I
23S-1714	1714–1731	CAAGTCGCTTCACCTACA	26	IV
23S-1732	1732–1749	TGATTTCAGCTCCACGAG	17	V
23S-1750	1750–1767	CCAGCTGGTATCTTCGAC	59	III
23S-1768	1768–1786	TTTTAATAAACAGTTGCAG	36	IV
23S-1787	1787–1804	GTTTGCACAGTGCTGTGT	57	III
23S-1805	1805–1822	GTATACGTCCACTTTCGT	58	III
23S-1823	1823–1839	CGGGCAGGCGTCACACC	58	III
23S-1840	1840–1857	CAATTAACCTTCCGGCAC	53	III
23S-1858	1858–1875	CGCTACCGCTAACCCCAT	12	V
23S-1876	1876–1893	GGCTTCGATCAAGAGCTT	8	V
23S-1894	1894–1910	CGGCCGCCGTTTACCGG	35	IV
23S-1911	1911–1928	TTAGGACCGTTATAGTTA	8	V
23S-1929	1929–1946	ACAAGGAATTTCGCTACC	56	III
23S-1936	1936–1953	TTACCCGACAAGGAATTT	28	IV
23S-1954	1954–1971	ATTCGTGCAGGTCGGAAC	59	III
23S-1965	1965–1982	ATCATTACGCCATTCGTG	58	III
23S-1983	1983–1999	GTGGAGACAGCCTGGCC	34	IV
23S-2000	2000–2017	AATTTCACTGAGTCTCGG	41	III
23S-2018	2018–2035	CATCTTCACAGCGAGTTC	100	I
23S-2036	2036–2053	CTTGCCGCGGGTACACTG	45	III
23S-2054	2054–2071	TTCACGGGGTCTTTCCGT	50	III
23S-2072	2072–2089	GTCAAGCTATAGTAAAGG	3	VI
23S-2090	2090–2107	CAAGGCTCAATGTTCAGT	3	VI
23S-2099	2099–2116	CCTACACATCAAGGCTCA	41	III
23S-2108	2108–2125	CCCACCTATCCTACACAT	63	II
23S-2117	2117–2134	TCAAAGCCTCCCACCTAT	22	IV
23S-2126	2126–2143	GTCCACACTTCAAAGCCT	3	VI
23S-2144	2144–2161	GGCTCCATGCAGACTGGC	3	VI
23S-2162	2162–2179	GGGTGGTATTTCAAGGTC	7	V
23S-2180	2180–2199	TTAGAACATCAAACATTAAA	1	VI
23S-2200	2200–2217	CCGGATTACGGGCCAACG	9	V
23S-2218	2218–2235	CCAGACACTGTCCGCAAC	48	III
23S-2227	2227–2244	AACTACCCACCAGACACT	48	III
23S-2236	2236–2253	CCCCAGTCAAACTACCCA	81	I
23S-2245	2245–2262	AGGAGACCGCCCCAGTCA	59	III
23S-2254	2254–2271	CTCTTTAGGAGGAGACCG	10	V
23S-2263	2263–2280	CCTCCGTTACTCTTTAGG	47	III
23S-2272	2272–2289	CTTCGTGCTCCTCCGTTA	75	II
23S-2290	2290–2307	CGACCAGGATTAGCCAAC	24	IV
23S-2308	2308–2325	CACTAACCTCCTGATGTC	61	II
23S-2326	2326–2343	AGCTGGCTTATGCCATTG	50	III
23S-2344	2344–2361	CCGTCACGCTCGCAGTCA	71	II
23S-2362	2362–2379	CTTTCGCACCTGCTCGCG	64	II
23S-2380	2380–2397	CCGGATCACTATGACCTG	62	II
23S-2398	2398–2415	CCCTTCCATTCAGAACCA	63	II
23S-2416	2416–2433	TTATCCGTTGAGCGATGG	31	IV
23S-2434	2434–2451	TTATCCCCGGAGTACCTT	45	III
23S-2452	2452–2469	TTGGGCGGTATCAGCCTG	23	IV
23S-2470	2470–2487	CGCCGTCGATATGAACTC	10	V
23S-2488	2488–2505	CATCGAGGTGCCAAACAC	13	V
23S-2506	2506–2523	CAGGATGTGATGAGCCGA	16	V
23S-2514	2514–2531	TTCAGCCCCAGGATGTGA	14	V
23S-2532	2532–2549	CATACCCTTGGGACCTAC	19	V
23S-2542	2542–2559	GGCGAACAGCCATACCCT	19	V
23S-2560	2560–2577	TCGCGTACCACTTTAAAT	43	III
23S-2578	2578–2595	CGACGTTCTAAACCCAGC	45	III
23S-2596	2596–2613	AGGGACCGAACTGTCTCA	55	III
23S-2614	2614–2630	CAGCGCCCACGGCAGAT	23	IV
23S-2631	2631–2648	CAGCCCCCCTCAGTTCTC	67	II
23S-2649	2649–2666	GTCCTCTCGTACTAGGAG	51	III
23S-2667	2667–2684	AGTGATGCGTCCACTCCG	44	III
23S-2685	2685–2702	CATGACAACCCGAACACC	9	V
23S-2703	2703–2720	ACCGGGCAGTGCCATTGG	21	IV
23S-2721	2721–2738	TCTCTTCCGCATTTAGCT	59	III
23S-2739	2739–2756	AGATGCTTTCAGCACTTA	5	VI
23S-2757	2757–2774	GGGGCAAGTTTCGTGCTT	27	IV
23S-2775	2775–2792	TCAGGGAGAACTCATCTC	37	IV
23S-2781	2781–2798	TAAGTCTCAGGGAGAACT	12	V
23S-2799	2799–2816	CGTTCCTTCAGGAGACTC	51	III
23S-2811	2811–2828	CGTCGTCTTCAACGTTCC	60	III
23S-2829	2829–2846	CACCCGGCCTATCAACGT	60	III
23S-2840	2840–2857	CTGCGCTTACACACCCGG	58	III
23S-2858	2858–2875	GGTTAGCTCAACGCATCG	60	III
23S-2865	2865–2882	TAGTACCGGTTAGCTCAA	48	III
23S-2883	2883–2900	TTAAGCCTCACGGTTCAT	44	III
23S-2887	2887–2904	AAGGTTAAGCCTCACGGT	36	IV

^aE. coli position according to the numbering of Brosius et al. (5). 

^bFluorescence intensities expressed as a percentage of that of the brightest probe detected, 23S-2018.