Table 3.

Quantitation of A/T track frequency, hairpin frequency and distance relationships across the genome

	A/T tracks > 9 bp		A/T tracks > 20 bp		Stable hairpin minimaa		Mean distance (bp): A/T tracks > 9bp		Mean distance (bp): A/T tracks > 20 bp
	Genic	Intergenic	Genic	Intergenic	Genic	Intergenic	Genic	Intergenic	Genic	Intergenic
Chr. 1	434	1223	70	250	566	958	269	103.0	145.3	101.3
Chr. 2	742	1629	93	371	915	1484	254.1	99.6	160.6	115.4
Chr. 3	962	1824	126	401	1117	1568	249.5	98.8	143.8	105.9
Chr. 4	1040	2005	106	460	1270	1734	318.8	107.3	195.5	110.9
Chr. 5	1085	2404	131	576	1307	2085	287.1	92.5	143.0	101.9
Chr. 6	1155	2365	143	526	1447	2449	299.8	92.1	193.5	95.9
Chr. 7	1292	2350	153	532	1558	2037	302.6	102.7	190.9	105.8
Chr. 8	1274	2722	146	631	1562	2466	274.6	99.4	173.6	105.8
Chr. 9	1286	2977	167	675	1543	2604	234.3	103.3	120.3	100.3
Chr. 10	1336	3160	175	710	1657	3009	266.0	99.4	152.2	101.7
Chr. 11	1746	3821	219	858	2060	3477	273.9	95.3	170.1	100.5
Chr. 12	1935	4169	239	989	2273	3655	272.1	97.7	151.1	98.2
Chr. 13	2336	5321	283	1197	2870	4690	280.7	102.9	177.6	102.7
Chr. 14	2785	6056	359	1333	3297	5223	282.6	100.9	175.7	106.2
Total	19 408	42 026	2410	9509	23 442	37 439	277.3	99.2	163.8	103.8

^aStable hairpin minima were determined by identifying the most stably predicted structure, most negative ΔG. If contiguous windows had the same minimum, the windows were combined into the same structure feature for calculations. Distances between A/T tracks and stable hairpin minimum were calculated from the edge of A/T tracks to the edge of stable hairpin minima.