Supplementary Material For

Yilmaz L.S. and D. R. Noguera (2004). A mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization. Applied and Environmental Microbiology, 70(12): 7126-7139.

Table of Calculated Free Energy Changes (DG⁰) and Solvent Accessible Surface Area (DASA_ts) for All Probes in the 16S rRNA Accessibility Maps of Fuchs et al. (1998) and Behrens et al. (2003).

Probe characteristics				Flourescein-labeled probes^*		Cy3-labeled probes^**		Gibbs free energy changes (kcal/mol)										DASA_ts
Name	5'	3'	Sequence	Intensity	Brightness Class	Intensity	Brightness Class	DG⁰₁	DG⁰₂	DG⁰_3-i	DG⁰_3-ii	DG⁰_3-iii	DG⁰_3-iv	DG⁰_overall-i	DG⁰_overall-ii	DG⁰_overall-iii	DG⁰_overall-iv	(Å/residue)
Eco1	1	19	TGATCAAACTCTTCAATTT	1	VI	0.68	II	-12.4	1.6	-2.8	-1.5	-2.8	-2.8	-9.5	-10.7	-9.5	-9.5	63.51
Eco13	13	31	CAATCTGAGCCATGATCAA	35	IV	0.58	III	-16.2	1.0	-3.2	-3.2	-3.9	-3.9	-12.9	-12.9	-12.2	-12.2	18.78
Eco20	20	37	AGCGTTCAATCTGAGCCA	44	III	1.15	I	-19.0	0.9	-6.2	-6.2	-2.9	-2.9	-12.6	-12.6	-15.9	-15.9	23.57
Eco32	32	47	GCCTGCCGCCAGCGTT	42	III	0.54	III	-24.3	-0.0	-6.5	-7.2	-17.9	-27.2	-17.4	-16.7	-6.0	3.3	27.28
Eco38	38	54	GTGTTAGGCCTGCCGCC	68	II	0.55	III	-24.1	-1.2	-5.4	-4.3	-10.7	-20.8	-17.4	-18.5	-12.1	-2.0	7.15
Eco48	48	65	TCGACTTGCATGTGTTAG	76	II	0.54	III	-16.1	1.0	-6.1	-1.2	-10.0	-13.0	-9.9	-14.7	-6.0	-3.0	2.82
Eco55	55	72	TTACCGTTCGACTTGCAT	56	III	0.74	II	-17.7	1.8	-3.3	-1.2	-8.7	-12.6	-14.4	-16.4	-9.0	-5.1	2.59
Eco60	60	77	TCCTGTTACCGTTCGACT	66	II	-	-	-19.7	1.8	-3.3	-2.8	-4.2	-15.0	-16.4	-16.9	-15.5	-4.7	2.59
Eco63	63	80	GCTTCCTGTTACCGTTCG	67	II	-	-	-20.9	1.8	-3.1	-5.9	-16.3	-15.0	-17.7	-14.9	-4.6	-5.9	0.00
Eco66	66	83	GCTGCTTCCTGTTACCGT	62	II	0.77	II	-22.4	1.8	-4.4	-5.9	-6.1	-6.1	-18.0	-16.5	-16.3	-16.3	0.00
Eco70	70	88	AGCAAGCTGCTTCCTGTTA	48	III	-	-	-20.8	-1.1	-8.7	-6.4	-7.0	-7.0	-10.9	-13.2	-12.6	-12.6	0.00
Eco73	73	90	GCAGCAAGCTGCTTCCTG	27	IV	0.27	IV	-21.5	-1.9	-8.0	-6.1	-7.0	-7.0	-11.6	-13.5	-12.6	-12.6	0.00
Eco79	79	96	CAGCAAAGCAGCAAGCTG	3	VI	-	-	-16.9	-1.6	-12.3	-7.4	-7.0	-7.0	-3.0	-7.8	-8.3	-8.3	0.00
Eco84	84	101	TCGTCAGCAAAGCAGCAA	6	V	0.18	V	-17.0	0.0	-12.5	-9.0	-7.0	-7.0	-4.1	-7.5	-9.6	-9.6	0.96
Eco87	87	104	CACTCGTCAGCAAAGCAG	10	V	-	-	-17.1	0.4	-11.8	-8.3	-8.6	-8.6	-5.0	-8.5	-8.2	-8.2	9.40
Eco89	89	106	GCCACTCGTCAGCAAAGC	41	III	-	-	-20.2	1.0	-9.5	-8.3	-16.4	-21.6	-10.6	-11.8	-3.7	1.5	12.15
Eco91	91	108	CCGCCACTCGTCAGCAAA	70	II	0.82	I	-20.8	0.2	-9.1	-6.8	-12.0	-16.5	-11.4	-13.7	-8.5	-4.0	17.17
Eco102	102	118	ACTCACCCGTCCGCCAC	46	III	0.75	II	-23.6	1.8	-6.7	-5.6	-6.5	-8.6	-16.8	-17.9	-17.0	-14.9	22.93
Eco109	109	126	CAGACATTACTCACCCGT	40	IV	0.82	I	-18.5	1.4	-10.3	-5.4	-14.5	-14.5	-8.2	-13.1	-4.0	-4.0	5.47
Eco119	119	136	GGCAGTTTCCCAGACATT	27	IV	0.78	II	-20.2	1.0	-8.1	-9.1	-20.7	-22.1	-12.0	-11.0	0.6	2.0	21.69
Eco127	127	144	CTCCATCAGGCAGTTCC	47	III	0.73	II	-23.0	0.3	-6.6	-8.8	-21.6	-25.2	-16.1	-13.8	-1.1	2.5	24.50
Eco137	137	154	AGTTATCCCCCTCCATCA	35	IV	0.71	II	-22.8	2.5	-8.9	-9.8	-18.3	-24.7	-13.9	-13.0	-4.5	1.9	3.35
Eco145	145	162	TTTCCAGTAGTTATCCCC	66	II	0.79	II	-20.1	2.0	-9.0	-3.1	-10.4	-19.6	-11.1	-16.9	-9.7	-0.5	0.50
Eco155	155	172	TTAGCTACCGTTTCCAGT	46	III	0.99	I	-19.3	1.9	-8.4	-7.6	-7.6	-7.6	-10.9	-11.7	-11.7	-11.7	0.00
Eco163	163	180	ATGCGGTATTAGCTACCG	30	IV	0.32	IV	-18.0	-2.6	-8.2	-7.6	-14.7	-19.6	-7.2	-7.8	-0.7	4.2	10.19
Eco173	173	190	TTGCGACGTTATGCGGTA	39	IV	0.39	IV	-18.0	-0.4	-4.4	-4.5	-3.8	-14.0	-12.9	-12.8	-13.5	-3.3	21.54
Eco181	181	198	CTTTGGTCTTGCGACGTT	65	II	0.77	II	-18.7	0.3	-4.2	-3.7	-9.7	-10.1	-14.2	-14.8	-8.7	-8.3	24.79
Eco191	191	209	AAGGTCCCCCTCTTTGGTC	76	II	0.75	II	-24.5	-0.5	-4.5	-12.0	-10.9	-10.1	-19.3	-11.8	-12.9	-13.7	12.73
Eco199	199	215	GGCCCTAAGGTCCCCCT	61	II	0.67	II	-26.1	-0.2	-9.0	-8.3	-10.8	-10.9	-16.5	-17.2	-14.7	-14.6	0.00
Eco210	210	226	CGATGGCAAGAGGCCCG	5	VI	0.17	V	-19.9	-1.8	-12.2	-13.2	-18.7	-29.5	-5.8	-4.8	0.7	11.5	1.27
Eco216	216	233	GCACATCCGATGGCAAGA	21	IV	0.29	IV	-18.8	0.4	-11.1	-12.2	-27.1	-30.7	-7.4	-6.3	8.6	12.2	16.23
Eco227	227	243	TCCCATCTGGGCACATC	26	IV	0.32	IV	-20.3	-1.2	-12.9	-12.9	-22.0	-29.5	-6.1	-6.1	3.0	10.5	32.45
Eco234	234	251	CTAGCTAATCCCATCTGG	27	IV	0.63	II	-18.2	0.6	-12.1	-12.1	-22.3	-28.5	-5.9	-6.0	4.3	10.5	15.62
Eco244	244	261	ACCCCACCTACTAGCTAA	41	III	0.56	III	-20.3	1.9	-12.7	-14.5	-11.4	-11.4	-7.6	-5.7	-8.9	-8.9	27.14
Eco252	252	268	AGCCGTTACCCCACCTA	62	II	1.02	I	-22.6	2.2	-9.8	-9.7	-9.8	-9.8	-12.8	-12.9	-12.8	-12.8	44.51
Eco262	262	279	TCGCCTAGGTGAGCCGTT	19	V	0.16	V	-22.7	0.6	-12.0	-12.2	-11.4	-11.4	-10.5	-10.3	-11.1	-11.1	28.38
Eco269	269	285	GGATCGTCGCCTAGGTG	27	IV	0.32	IV	-19.8	1.5	-13.8	-14.8	-21.4	-26.8	-6.0	-4.9	1.6	7.0	21.63
Eco280	280	297	CAGACCAGCTAGGGATCG	25	IV	0.48	III	-19.0	-0.3	-13.3	-15.0	-14.4	-21.2	-5.1	-3.5	-4.0	2.8	6.94
Eco285	285	302	CCTCTCAGACCAGCTAGG	53	III	0.7	II	-20.9	0.0	-13.7	-14.7	-14.4	-20.9	-6.8	-5.7	-6.1	0.4	3.39
Eco298	298	315	TGTGGCTGGTCATCCTCT	56	III	0.82	I	-21.9	0.3	-8.3	-8.1	-8.2	-18.2	-13.3	-13.6	-13.4	-3.4	11.09
Eco303	303	320	TCCAGTGTGGCTGGTCAT	25	IV	0.52	III	-21.6	-2.1	-10.3	-10.6	-12.0	-26.9	-9.1	-8.8	-7.4	7.5	7.69
Eco316	316	333	ACCGTGTCTCAGTTCCAG	62	II	0.54	III	-20.7	2.0	-5.8	-6.1	-12.8	-12.8	-14.9	-14.6	-7.9	-7.9	20.84
Eco321	321	338	TCTGGACCGTGTCTCAGT	71	II	0.78	II	-20.7	0.4	-5.8	-6.1	-12.8	-12.8	-14.6	-14.3	-7.6	-7.6	20.84
Eco334	334	350	CTCCCGTAGGAGTCTGG	27	IV	0.48	III	-20.3	-1.3	-9.8	-10.0	-14.3	-21.4	-9.1	-8.9	-4.6	2.5	0.36
Eub338	338	353	GCTGCCTCCCGTAGGAGT	58	III	-	-	-22.2	-1.6	-5.4	-5.8	-10.1	-10.1	-15.2	-14.7	-10.5	-10.5	0.38
Eco343	343	359	CACTGCTGCCTCCCGTA	64	II	0.73	II	-22.8	1.9	-9.1	-5.4	-14.4	-19.2	-13.7	-17.4	-8.4	-3.6	0.36
Eco351	351	369	CAATATTCCCCACTGCTGC	33	IV	0.66	II	-21.3	1.6	-5.3	-5.0	-13.1	-14.4	-16.0	-16.3	-8.2	-6.9	13.50
Eco360	360	377	CCATTGTGCAATATTCCC	35	IV	0.69	II	-18.1	0.4	-10.1	-10.0	-12.6	-13.2	-7.8	-7.8	-5.3	-4.7	33.79
Eco370	370	386	GGCTTGCGCCCATTGTG	52	III	0.54	III	-21.9	-0.8	-11.5	-9.9	-11.0	-11.0	-9.4	-11.0	-9.9	-9.9	22.00
Eco378	378	394	CTGCATCAGGCTTGCGC	32	IV	1.09	I	-20.6	-0.3	-8.9	-10.1	-11.0	-11.0	-11.1	-9.9	-9.0	-9.0	13.18
Eco387	387	403	GCGGCATGGCTGCATCA	39	IV	0.4	IV	-21.4	-1.7	-6.1	-4.5	-14.0	-25.7	-13.5	-15.1	-5.6	6.1	26.12
Eco395	395	412	TTCATACACGCGGCATGG	35	IV	1.06	I	-18.3	1.4	-4.5	-4.4	-19.7	-24.5	-13.7	-13.8	1.5	6.3	46.11
Eco404	404	421	AAGGCCTTCTTCATACAC	37	IV	0.64	II	-17.0	0.5	-3.3	-4.9	-10.8	-17.2	-13.5	-11.9	-6.0	0.4	39.48
Eco413	413	429	TACAACCCGAAGGCCTTC	62	II	0.69	II	-17.9	-0.7	-4.8	-4.7	-4.7	-4.7	-12.3	-12.4	-12.4	-12.4	24.59
Eco422	422	439	AAAGTACTTTACAACCCG	37	IV	0.66	II	-13.5	0.6	-6.1	-4.9	-13.1	-17.2	-7.2	-8.5	-0.2	3.9	32.84
Eco431	431	448	TCCCCGCTGAAAGTACTT	42	III	0.33	IV	-19.2	0.7	-8.8	-8.1	-23.0	-27.2	-10.2	-10.9	4.0	8.2	11.30
Eco439	439	455	CCCTTCCTCCCCGCTGA	53	III	-	-	-26.1	2.1	-11.2	-10.0	-16.4	-22.7	-14.9	-16.1	-9.7	-3.4	10.21
Eco440	440	456	TCCCTTCCTCCCCGCTG	83	I	0.94	I	-26.0	4.6	-11.2	-10.0	-18.0	-24.3	-14.8	-16.1	-8.0	-1.7	8.58
Eco443	443	460	TTACTCCCTTCCTCCCCG	62	II	-	-	-24.9	4.6	-12.6	-11.8	-21.8	-32.3	-12.3	-13.1	-3.1	7.4	8.10
Eco446	446	463	ACTTTACTCCCTTCCTCC	64	II	-	-	-21.7	4.6	-10.3	-10.3	-10.3	-10.3	-11.4	-11.4	-11.4	-11.4	8.10
Eco449	449	467	ATTAACTTTACTCCCTTCC	35	IV	0.47	III	-18.1	1.8	-6.7	-6.8	-6.7	-6.7	-11.3	-11.2	-11.3	-11.3	7.53
Eco455	455	473	AAAGGTATTAACTTTACTC	3	VI	0.01	VI	-11.4	0.4	-6.7	-6.8	-6.7	-6.7	-4.4	-4.2	-4.4	-4.4	0.15
Eco468	468	486	AACGTCAATGAGCAAAGGT	3	VI	0.03	VI	-14.6	1.2	-6.7	-6.8	-6.7	-6.7	-7.9	-7.7	-7.9	-7.9	6.24
Eco474	474	491	CGGGTAACGTCAATGAGC	3	VI	0.25	IV	-16.4	0.3	-9.8	-10.3	-24.1	-28.8	-6.3	-5.8	8.0	12.7	9.00
Eco478	478	495	TCTGCGGGTAACGTCAAT	20	V	-	-	-17.2	-0.2	-6.0	-7.7	-17.1	-18.9	-10.6	-9.0	0.5	2.3	4.15
Eco481	481	498	TCTTCTGCGGGTAACGTC	21	IV	-	-	-18.9	-0.2	-6.0	-7.7	-17.1	-18.9	-12.3	-10.7	-1.3	0.5	5.28
Eco484	484	501	GCTTCTTCTGCGGGTAAC	60	III	-	-	-19.4	1.6	-6.9	-9.7	-21.5	-25.5	-12.5	-9.7	2.1	6.1	9.72
Eco487	487	504	GGTGCTTCTTCTGCGGGT	54	III	0.72	II	-22.8	1.0	-8.1	-8.8	-21.2	-29.0	-14.5	-13.8	-1.5	6.3	17.70
Eco492	492	509	TAGCCGGTGCTTCTTCTG	46	III	0.63	II	-20.7	-1.0	-7.5	-8.2	-15.2	-15.2	-12.1	-11.4	-4.4	-4.4	23.88
Eco499	499	516	ACGGAGTTAGCCGGTGCT	25	IV	-	-	-21.7	-1.3	-7.8	-8.5	-18.4	-22.7	-12.5	-11.9	-1.9	2.4	29.55
Eco505	505	522	GCTGGCACGGAGTTAGCC	56	III	0.4	IV	-22.4	-0.8	-8.9	-9.0	-4.3	-4.3	-12.5	-12.4	-17.1	-17.1	36.75
Eco510	510	527	CGGCTGCTGGCACGGAGT	37	IV	0.41	III	-23.2	-0.5	-6.8	-8.2	-4.3	-4.3	-15.7	-14.3	-18.2	-18.2	41.27
Eco523	523	540	CTCCGTATTACCGCGGCT	54	III	0.76	II	-22.2	-0.8	-6.3	-8.2	-4.3	-4.3	-14.9	-13.0	-16.9	-16.9	35.70
Eco528	528	545	GCACCCTCCGTATTACCG	42	III	0.49	III	-22.4	0.8	-9.1	-9.4	-13.5	-27.4	-13.1	-12.8	-8.7	5.2	40.06
Eco541	541	558	CCGATTAACGCTTGCACC	96	I	0.66	II	-18.8	-0.0	-2.2	-2.2	-2.8	-4.0	-16.1	-16.1	-15.5	-14.3	44.70
Eco548	548	566	CAGTAATTCCGATTAACGC	42	III	0.45	III	-15.3	-0.0	-0.2	-1.0	0.1	0.1	-14.3	-13.7	-14.4	-14.4	38.23
Eco559	559	576	GCTTTACGCCCAGTAATT	46	III	0.49	III	-18.5	0.0	-4.1	-4.9	6.3	6.3	-14.0	-13.2	-18.1	-18.1	24.39
Eco567	567	584	CTGCGTGCGCTTTACGCC	44	III	0.73	II	-22.7	-2.2	-4.1	-4.1	0.7	0.7	-16.3	-16.3	-20.3	-20.3	14.98
Eco577	577	594	AACAAACCGCCTGCGTGC	42	III	0.78	II	-19.8	0.2	-7.0	-6.1	-13.4	-24.1	-12.4	-13.3	-6.0	4.7	35.16
Eco585	585	602	TCTGACTTAACAAACCGC	2	VI	0.14	V	-14.3	1.9	-10.1	-8.4	-19.8	-28.7	-4.2	-5.9	5.5	14.4	43.04
Eco595	595	613	GGGATTTCACATCTGACTT	2	VI	0.1	V	-17.5	0.5	-13.3	-15.0	-20.5	-28.7	-4.0	-2.2	3.3	11.4	27.60
Eco603	603	620	GAGCCCGGGGATTTCACA	4	VI	0.19	V	-21.7	0.5	-13.2	-13.2	-13.2	-13.2	-8.3	-8.3	-8.3	-8.3	26.13
Eco614	614	631	GTTCCCAGGTTGAGCCCG	25	IV	0.34	IV	-24.3	0.2	-8.3	-8.3	-8.5	-8.5	-15.6	-15.6	-15.4	-15.4	34.45
Eco621	621	638	AGATGCAGTTCCCAGGTT	2	VI	0.04	VI	-20.5	2.0	-12.3	-15.8	-17.5	-17.5	-8.2	-4.7	-3.0	-3.0	24.20
Eco627	627	644	AGTATCAGATGCAGTTCC	1	VI	0.18	V	-17.5	1.6	-9.6	-15.7	-19.5	-17.5	-7.8	-1.7	2.1	0.1	26.58
Eco632	632	649	TTGCCAGTATCAGATGCA	2	VI	0.04	VI	-18.1	0.5	-8.3	-11.0	-22.6	-17.5	-9.6	-6.8	4.7	-0.3	24.93
Eco639	639	656	CTCAAGCTTGCCAGTATC	4	VI	0.09	V	-18.4	0.9	-10.1	-12.2	-19.3	-21.0	-8.2	-6.1	1.1	2.7	27.99
Eco645	645	662	ACGAGACTCAAGCTTGCC	22	IV	0.81	I	-18.5	0.9	-10.1	-10.8	-17.4	-25.3	-8.3	-7.6	-1.0	6.9	23.03
Eco650	650	667	CCTCTACGAGACTCAAGC	13	V	0.36	IV	-17.7	0.2	-11.7	-12.1	-22.8	-26.1	-5.6	-5.3	5.4	8.8	32.53
Eco654	654	671	CCCCCCTCTACGAGACTC	17	V	-	-	-23.7	0.2	-8.0	-10.9	-26.8	-31.4	-15.3	-12.4	3.5	8.1	36.56
Eco657	657	674	CTACCCCCCTCTACGAGA	19	V	0.47	III	-22.9	0.2	-6.6	-10.9	-29.3	-33.5	-15.9	-11.6	6.8	11.0	45.39
Eco661	661	678	AATTCTACCCCCCTCTAC	22	IV	-	-	-20.9	3.2	-7.8	-13.1	-23.7	-29.5	-13.1	-7.8	2.8	8.6	44.34
Eco665	665	682	CTGGAATTCTACCCCCCT	21	IV	1.14	I	-22.2	1.2	-11.9	-16.1	-27.7	-35.6	-10.2	-6.0	5.5	13.4	40.01
Eco668	668	685	CACCTGGAATTCTACCCC	12	V	0.82	I	-20.3	1.2	-10.5	-14.6	-27.3	-32.7	-9.7	-5.5	7.1	12.5	43.17
Eco675	675	692	ACCGCTACACCTGGAATT	50	III	0.62	II	-18.6	0.2	-7.3	-7.7	-11.9	-11.9	-10.9	-10.5	-6.3	-6.3	44.85
Eco681	681	698	CATTTCACCGCTACACCT	55	III	1.3	I	-19.5	4.6	-7.3	-6.7	-7.2	-7.2	-12.2	-12.8	-12.2	-12.2	43.74
Eco686	686	703	CTACGCATTTCACCGCTA	40	IV	0.67	II	-18.8	0.9	-2.2	-2.2	-2.2	-2.2	-16.4	-16.4	-16.4	-16.4	34.68
Eco690	690	707	ATCTCTACGCATTTCACC	60	III	1.27	I	-17.7	3.2	-4.3	-4.3	-4.3	-4.3	-13.4	-13.4	-13.4	-13.4	37.38
Eco693	693	710	CAGATCTCTACGCATTTC	29	IV	0.44	III	-16.2	0.8	-4.8	-6.7	-10.7	-10.7	-11.1	-9.3	-5.3	-5.3	29.86
Eco704	704	721	CGGTATTCCTCCAGATCT	38	IV	0.75	II	-19.7	0.6	-7.5	-5.5	-15.1	-16.7	-11.9	-13.9	-4.4	-2.7	51.11
Eco711	711	728	TCGCCACCGGTATTCCTC	62	II	0.65	II	-22.7	0.3	-7.8	-5.0	-4.3	-4.3	-14.6	-17.4	-18.1	-18.1	36.28
Eco722	722	737	GGGCCGCCTTCGCCTC	21	IV	0.64	II	-24.9	-0.6	-8.4	-8.5	-11.7	-11.7	-15.6	-15.5	-12.4	-12.4	32.46
Eco729	729	744	GTCCAGGGGGCCGCCT	37	IV	0.25	IV	-25.3	0.0	-8.4	-9.8	-16.1	-11.7	-16.4	-15.0	-8.7	-13.2	55.59
Eco738	738	755	CGTCAGTCTTCGTCCAGG	19	V	0.67	II	-20.9	1.5	-6.0	-7.3	-24.8	-30.7	-14.8	-13.5	4.0	9.8	48.87
Eco745	745	762	ACCTGAGCGTCAGTCTTC	19	V	0.33	IV	-20.2	-0.4	-9.0	-6.5	-15.7	-22.5	-10.6	-13.0	-3.8	2.9	24.53
Eco756	756	773	CACGCTTTCGCACCTGAG	15	V	0.53	III	-20.0	0.1	-11.1	-9.5	-14.8	-28.1	-8.5	-10.2	-4.8	8.4	6.15
Eco763	763	780	TGCTCCCCACGCTTTCGC	77	II	0.79	II	-24.8	0.1	-8.3	-9.8	-20.1	-23.9	-16.1	-14.5	-4.2	-0.5	14.22
Eco774	774	791	CTAATCCTGTTTGCTCCC	52	III	0.57	III	-20.1	1.3	-6.5	-7.2	-5.7	-5.7	-13.5	-12.8	-14.3	-14.3	9.76
Eco781	781	799	CAGGGTATCTAATCCTGTT	4	VI	0.25	IV	-18.1	-1.2	-5.2	-3.2	-4.6	-4.6	-11.6	-13.6	-12.2	-12.2	4.02
Eco792	792	809	CGTGGACTACCAGGGTAT	2	VI	0.35	IV	-19.0	-0.1	-8.2	-9.5	-14.3	-15.1	-10.4	-9.1	-4.2	-3.4	6.56
Eco800	800	817	GTTTACGGCGTGGACTAC	31	IV	0.37	IV	-18.1	1.3	-5.2	-6.4	-10.8	-16.7	-12.9	-11.6	-7.3	-1.4	2.32
Eco810	810	827	AGTCGACATCGTTTACGG	38	IV	0.5	III	-16.5	0.0	-7.1	-8.1	-15.3	-15.3	-9.0	-8.0	-0.8	-0.8	13.64
Eco818	818	835	AACCTCCAAGTCGTCATC	10	V	0.62	II	-18.2	1.3	-7.0	-8.5	-17.5	-25.8	-11.1	-9.6	-0.6	7.7	30.61
Eco828	828	845	TCAAGGGCACAACCTCCA	6	V	0.56	III	-19.8	-0.4	-7.0	-11.4	-18.9	-25.8	-12.1	-7.7	-0.3	6.7	23.66
Eco836	836	852	CCACGCCTCAAGGGCAC	8	V	0.15	V	-21.2	-1.9	-10.1	-10.1	-9.4	-9.4	-9.2	-9.2	-9.9	-9.9	10.00
Eco846	846	862	GCTCCGGAAGCCACGCC	42	III	0.39	IV	-23.5	-0.4	-11.8	-11.8	-10.6	-11.0	-11.1	-11.0	-12.2	-11.8	6.19
Eco853	853	870	ACGCGTTAGCTCCGGAAG	52	III	0.21	IV	-19.5	0.1	-8.7	-10.1	-12.0	-12.0	-10.4	-9.0	-7.1	-7.1	5.74
Eco863	863	880	GGTCGACTTAACGCGTTA	42	III	0.39	IV	-17.0	0.7	-6.4	-5.3	-12.9	-15.3	-10.4	-11.5	-4.0	-1.6	26.90
Eco871	871	888	CCCCAGGCGGTCGACTTA	87	I	0.73	II	-23.6	0.6	-5.9	-6.3	5.2	5.2	-17.5	-17.1	-23.4	-23.4	30.71
Eco881	881	897	GGCCGTACTCCCCAGGC	77	II	0.77	II	-25.4	-0.6	-8.4	-8.7	1.7	1.7	-16.2	-15.8	-24.5	-24.5	6.84
Eco889	889	906	TAACCTTGCGGCCGTACT	85	I	0.62	II	-20.5	0.4	-4.9	-6.2	-4.1	-4.1	-15.4	-14.0	-16.2	-16.2	0.00
Eco898	898	916	ATTTGAGTTTTAACCTTGC	73	II	0.52	III	-15.4	1.0	-5.4	-5.5	-3.4	-4.2	-9.9	-9.8	-11.9	-11.1	13.73
Eco907	907	925	CGTCAATTCATTTGAGTTT	40	IV	1.01	I	-14.9	-0.3	-1.3	-2.9	1.7	1.7	-12.9	-11.3	-14.2	-14.2	21.00
Eco917	917	933	CGGGCCCCCGTCAATTC	69	II	0.6	III	-23.1	-1.0	-9.1	-8.2	-10.3	-10.3	-12.8	-13.7	-11.6	-11.6	16.28
Eco926	926	941	CGCTTGTGCGGGCCCC	38	IV	0.53	III	-24.2	-1.4	-10.9	-10.0	-20.6	-28.9	-11.8	-12.8	-2.1	6.1	18.28
Eco934	934	951	CATGCTCCACCGCTTGTG	50	III	0.88	I	-21.7	-0.1	-10.4	-9.3	-19.5	-27.5	-10.8	-11.8	-1.6	6.3	27.44
Eco942	942	959	TTAAACCACATGCTCCAC	46	III	0.72	II	-16.3	1.9	-7.6	-4.8	-17.1	-21.5	-8.7	-11.4	0.9	5.3	34.53
Eco952	952	969	TTGCATCGAATTAAACCA	4	VI	0.25	IV	-12.8	1.9	-5.5	-6.2	-11.3	-21.5	-7.3	-6.5	-1.4	8.7	26.77
Eco960	960	977	TCTTCGCGTTGCATCGAA	60	III	0.46	III	-18.1	0.0	-5.9	-2.1	-11.3	-21.5	-11.8	-15.5	-6.4	3.8	35.35
Eco970	970	987	CAGGTAAGGTTCTTCGCG	33	IV	0.47	III	-18.1	0.9	-7.4	-5.0	-9.8	-21.5	-10.5	-12.9	-8.1	3.5	44.99
Eco978	978	995	GTCAAGACCAGGTAAGGT	27	IV	0.22	IV	-17.3	-0.3	-8.2	-4.1	-15.9	-15.9	-8.5	-12.6	-0.8	-0.8	24.80
Eco988	988	1005	TTCCGTGGATGTCAAGAC	8	V	0.26	IV	-17.0	1.0	-7.2	-5.3	-17.0	-20.4	-9.6	-11.5	0.1	3.5	4.03
Eco996	996	1013	CTGAAAACTTCCGTGGAT	10	V	0.2	V	-14.7	0.8	-8.3	-8.3	-19.5	-25.0	-6.3	-6.2	5.0	10.4	0.00
Eco1006	1006	1023	ATTCTCATCTCTGAAAAC	4	VI	0.06	V	-12.2	0.8	-6.7	-6.2	-7.3	-7.3	-5.4	-5.8	-4.7	-4.7	6.09
Eco1014	1014	1031	GAAGGCACATTCTCATCT	8	V	0.16	V	-16.8	1.3	-8.4	-7.2	-6.3	-7.4	-8.3	-9.5	-10.4	-9.3	6.09
Eco1024	1024	1041	CACGGTTCCCGAAGGCAC	31	IV	0.6	III	-21.1	-1.6	-10.1	-4.6	-10.3	-10.3	-9.3	-14.8	-9.2	-9.2	0.00
Eco1032	1032	1049	ACCTGTCTCACGGTTCCC	52	III	0.57	III	-23.0	0.6	-10.1	-5.1	-14.6	-20.7	-12.7	-17.7	-8.2	-2.1	7.85
Eco1042	1042	1059	GCCATGCAGCACCTGTCT	48	III	0.6	III	-23.5	0.5	-9.7	-5.6	-10.5	-17.1	-13.5	-17.6	-12.7	-6.1	31.83
Eco1050	1050	1067	TGACGACAGCCATGCAGC	6	V	0.35	IV	-20.0	0.4	-6.6	-3.5	-8.6	-15.7	-13.2	-16.2	-11.1	-4.0	38.27
Eco1060	1060	1077	CAACACGAGCTGACGACA	2	VI	0.15	V	-16.1	-0.3	-9.7	-6.3	-14.5	-24.0	-5.8	-9.1	-1.0	8.6	37.71
Eco1068	1068	1085	ACATTTCACAACACGAGC	12	V	0.2	V	-14.8	2.1	-6.4	-6.9	-17.6	-17.6	-8.4	-7.8	2.8	2.8	39.39
Eco1078	1078	1095	ACTTAACCCAACATTTCA	6	V	0.18	V	-14.7	1.9	-3.2	-4.5	-2.7	-2.7	-11.4	-10.1	-11.9	-11.9	18.94
Eco1086	1086	1103	GTTGCGGGACTTAACCCA	10	V	0.27	IV	-20.1	-0.9	-5.1	-6.6	-8.5	-9.8	-13.9	-12.4	-10.5	-9.2	23.91
Eco1097	1097	1112	GTTGCGCTCGTTGCGGG	6	V	0.27	IV	-19.7	-2.2	-6.8	-5.5	-11.3	-20.5	-10.6	-11.9	-6.1	3.0	53.14
Eco1104	1104	1121	AGGATAAGGGTTGCGCTC	8	V	0.38	IV	-18.6	1.6	-6.2	-8.9	-22.5	-27.0	-12.3	-9.7	4.0	8.5	51.16
Eco1113	1113	1130	TGGCAACAAAGGATAAGG	2	VI	0.03	VI	-12.4	-0.2	-4.7	-6.5	-14.7	-23.1	-7.1	-5.3	2.8	11.2	49.19
Eco1122	1122	1139	CCGGACCGCTGGCAACAA	15	V	0.27	IV	-21.1	-0.2	-7.6	-8.1	-8.2	-8.2	-12.9	-12.5	-12.4	-12.4	29.36
Eco1131	1131	1146	TTCCCGGCCGGACCGC	40	IV	0.48	III	-24.0	-1.7	-6.1	-6.1	-4.6	-4.6	-16.1	-16.1	-17.6	-17.6	4.33
Eco1140	1140	1157	TCTCCTTTGAGTTCCCGG	46	III	0.77	II	-21.5	0.1	-6.8	-9.3	-14.7	-4.6	-14.3	-11.8	-6.4	-16.5	26.39
Eco1147	1147	1165	ACTGGCAGTCTCCTTTGAG	13	V	0.19	V	-20.8	0.3	-5.7	-11.9	-15.5	-4.6	-14.7	-8.6	-4.9	-15.8	26.91
Eco1158	1158	1175	CCAGTTTATCACTGGCAG	2	VI	0.03	VI	-18.2	-2.3	-6.9	-6.9	-8.9	-8.9	-8.9	-8.9	-6.9	-6.9	4.86
Eco1166	1166	1183	ACCTTCCTCCAGTTTATC	10	V	0.32	IV	-19.7	2.0	-6.9	-6.9	-8.9	-8.9	-12.8	-12.8	-10.7	-10.7	13.74
Eco1176	1176	1193	CGTCATCCCCACCTTCCT	50	III	0.84	I	-24.8	2.5	-7.8	-7.8	-10.3	-13.0	-17.0	-16.9	-14.5	-11.8	45.86
Eco1184	1184	1201	TGACTTGACGTCATCCCC	6	V	0.12	V	-20.3	-0.7	-6.8	-8.2	-9.2	-12.8	-12.6	-11.2	-10.2	-6.6	42.32
Eco1194	1194	1211	AGGGCCATGATGACTTGA	10	V	0.25	IV	-18.2	1.1	-11.3	-7.1	-10.9	-17.1	-6.8	-10.9	-7.2	-1.0	30.36
Eco1202	1202	1219	TGGTCGTAAGGGCCATGA	2	VI	0.05	VI	-19.5	-0.8	-9.5	-6.6	-17.0	-24.1	-9.0	-12.0	-1.6	5.5	31.92
Eco1212	1212	1229	TGTGTAGCCCTGGTCGTA	25	IV	0.63	II	-21.8	1.8	-7.0	-8.3	-14.7	-22.9	-14.8	-13.4	-7.0	1.2	53.30
Eco1220	1220	1237	GTAGCACGTGTGTAGCCC	58	III	0.62	II	-21.9	0.5	-7.0	-8.3	-15.8	-24.4	-14.7	-13.4	-5.9	2.7	55.66
Eco1230	1230	1247	ATGCGCCATTGTAGCACG	35	IV	0.36	IV	-19.6	-0.1	-6.4	-7.7	-22.6	-31.9	-12.7	-11.4	3.5	12.9	31.10
Eco1238	1238	1255	CTCTTTGTATGCGCCATT	31	IV	0.68	II	-18.8	0.8	-5.1	-5.9	-15.6	-21.5	-13.6	-12.7	-3.1	2.9	41.47
Eco1248	1248	1265	GAGGTCGCTTCTCTTTGT	58	III	0.61	II	-19.8	0.6	-1.3	-5.9	-5.9	-5.9	-18.2	-13.7	-13.7	-13.7	24.35
Eco1256	1256	1273	GCTCTCGCGAGGTCGCTT	62	II	0.58	III	-23.1	-1.8	-5.0	-5.9	-6.2	-6.2	-16.3	-15.4	-15.1	-15.1	2.36
Eco1266	1266	1283	AGGTCCGCTTGCTCTCGC	58	III	0.52	III	-23.9	0.6	-4.1	-5.9	-5.9	-5.9	-19.5	-17.7	-17.7	-17.7	13.36
Eco1274	1274	1291	ACTTTATGAGGTCCGCTT	15	V	0.26	IV	-18.4	0.4	-2.4	-5.1	-5.9	-5.9	-15.7	-13.0	-12.2	-12.2	22.08
Eco1284	1284	1301	ACTACGACGCACTTTATG	15	V	0.33	IV	-14.9	1.0	-3.2	-5.3	-15.6	-19.8	-11.6	-9.5	0.9	5.0	20.87
Eco1292	1292	1309	CAATCCGGACTACGACGC	23	IV	0.42	III	-17.9	-0.7	-5.6	-7.4	-16.3	-20.2	-11.4	-9.5	-0.7	3.2	40.13
Eco1302	1302	1319	TTGCAGACTCCAATCCGG	33	IV	0.56	III	-19.2	0.5	-7.8	-8.3	-8.7	-17.3	-11.1	-10.6	-10.3	-1.7	59.20
Eco1310	1310	1327	GAGTCGAGTTGCAGACTC	2	VI	0.02	VI	-18.1	-0.9	-9.3	-8.3	-10.8	-10.8	-7.8	-8.7	-6.3	-6.3	51.13
Eco1320	1320	1337	CGACTTCATGGAGTCGAG	6	V	0.01	VI	-16.7	-2.9	-6.7	-8.8	-6.8	-17.3	-7.1	-5.0	-7.0	3.5	36.55
Eco1328	1328	1345	AGCGATTCCGACTTCATG	65	II	0.65	II	-17.5	-0.4	-8.6	-8.4	-9.7	-13.7	-8.2	-8.4	-7.1	-3.1	30.73
Eco1338	1338	1355	CACGATTACTAGCGATTC	15	V	0.16	V	-14.7	0.1	-4.4	-11.7	-10.2	-16.4	-9.9	-2.6	-4.1	2.1	43.64
Eco1346	1346	1363	TTCTGATCCACGATTACT	12	V	0.51	III	-15.9	0.8	-0.4	-7.5	-14.2	-16.4	-15.1	-8.2	-1.5	0.7	40.24
Eco1356	1356	1373	CACCGTGGCATTCTGATC	19	V	0.43	III	-19.3	0.9	-6.7	-7.5	-15.6	-16.4	-12.5	-11.6	-3.6	-2.7	51.27
Eco1364	1364	1382	GAACGTATTCACCGTGGCA	21	IV	0.56	III	-19.6	-0.2	-8.4	-10.3	-9.6	-16.4	-10.6	-8.7	-9.4	-2.6	70.54
Eco1374	1374	1391	AAGGCCCGGGAACGTATT	52	III	0.58	III	-19.2	-0.9	-1.3	-3.2	-18.4	-21.1	-16.7	-14.9	0.3	3.0	35.85
Eco1383	1383	1400	GGTGTGTACAAGGCCCGG	65	II	0.58	III	-21.9	0.8	-4.0	-5.5	-10.3	-10.3	-17.7	-16.2	-11.4	-11.4	6.11
Eco1392	1392	1409	GTGACGGGCGGTGTGTAC	67	II	0.48	III	-20.8	0.2	-5.2	-5.1	0.4	0.4	-15.3	-15.4	-20.2	-20.2	4.13
Eco1401	1401	1418	TCCCATGGTGTGACGGGC	67	II	0.64	II	-22.7	-0.3	-6.1	-5.7	-5.3	-5.3	-16.0	-16.4	-16.8	-16.8	2.51
Eco1410	1410	1427	GCAACCCACTCCCATGGT	90	I	0.52	III	-23.4	0.1	-9.2	-8.8	-25.3	-5.3	-13.8	-14.2	2.4	-17.6	2.51
Eco1419	1419	1436	ACTTCTTTTGCAACCCAC	23	IV	0.46	III	-18.0	1.5	-5.6	-6.2	-23.5	-5.3	-12.3	-11.8	5.6	-12.6	1.18
Eco1428	1428	1445	AAGCTACCTACTTCTTTT	38	IV	0.66	II	-15.8	1.0	-5.9	-7.2	-16.0	-5.3	-9.8	-8.5	0.3	-10.4	7.78
Eco1437	1437	1454	CCGAAGGTTAAGCTACCT	4	VI	0.04	VI	-17.7	-0.6	-8.4	-8.2	-10.2	-10.2	-8.5	-8.8	-6.8	-6.8	6.60
Eco1446	1446	1463	AGCGCCCTCCCGAAGGTT	44	III	0.59	III	-24.8	-0.7	-7.4	-7.3	-9.1	-9.1	-16.6	-16.6	-14.8	-14.8	18.42
Eco1455	1455	1472	AAAGTGGTAAGCGCCCTC	31	IV	0.69	II	-19.0	0.6	-10.0	-8.5	-10.5	-10.5	-8.8	-10.2	-8.2	-8.2	18.42
Eco1464	1464	1481	ATGAATCACAAAGTGGTA	4	VI	0.03	VI	-12.0	0.3	-4.5	-3.1	-24.5	-10.5	-7.2	-8.6	12.8	-1.1	0.00
Eco1473	1473	1490	ACCCCAGTCATGAATCAC	65	II	0.66	II	-18.6	0.6	-4.6	-3.1	-24.2	-10.5	-13.8	-15.3	5.9	-7.8	0.83
Eco1482	1482	1499	TACGACTTCACCCCAGTC	100	I	0.56	III	-20.3	0.5	-4.7	-4.2	-3.4	-5.3	-15.4	-15.8	-16.6	-14.7	5.81
Eco1491	1491	1508	TTACCTTGTTACGACTTC	31	IV	0.39	IV	-15.6	1.0	-7.0	-7.5	-4.0	-4.0	-8.5	-7.9	-11.5	-11.5	4.98
Eco1500	1500	1517	CCCCTACGGTTACCTTGT	92	I	0.51	III	-22.3	0.9	-12.3	-14.3	-12.5	-14.4	-9.8	-7.9	-9.7	-7.7	0.00
Eco1509	1509	1525	CGCAGGTTCCCCTACGG	4	VI	0.13	V	-22.3	-0.6	-12.3	-14.4	-17.5	-17.5	-9.2	-7.1	-4.0	-4.0	6.84
Eco1518	1518	1535	GTGATCCAACCGCAGGTT	17	V	0.17	V	-20.3	-2.5	-11.8	-13.8	-13.8	-14.4	-6.1	-4.0	-4.0	-3.4	6.84
Eco1526	1526	1542	TAAGGAGGTGATCCAAC	25	IV	0.29	IV	-14.0	-1.0	-5.0	-5.8	-5.2	-5.2	-7.9	-7.1	-7.6	-7.6	0.00

^* Fuchs, B., Wallner, G., Beisker, W., Schwippl, I., Ludwig, W., and Amann, R. (1998). "Flow Cytometric Analysis of the In Situ Accessibility of Escherichia coli 16S rRNA for Fluorescently Labeled Oligonucleotide Probes." Applied and Environmental Microbiology, 64(12), 4973-4982.

** Behrens, S., Rühland, C., Inácio, J., Huber, H., Fonseca, A., Spencer-Martins, I., Fuchs, B., and Amann, R. (2003). "In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria, Archaea, and Eucarya to Cy3-Labeled Oligonucleotide Probes." Applied and Environmental Microbiology, 69, 1748-1758.

University of Wisconsin-Madison

Department of Civil and Environmental Engineering

3216 Engineering Hall

1415 Engineering Drive, Madison, WI 53706

Email: noguera@engr.wisc.edu

This page was created on March 24, 2004. Last revision was on December 06, 2008