Table 6.

The distribution of SSRs in different genomic regions

	All SSR loci				SSR loci with unique flanking sequences				SSR loci with polymorphism
	Count	Interval (kb)	Length (bp)	GC%	Count	Interval (kb)	Length (bp)	GC%	Count	Interval (kb)	Length (bp)	GC%
B73
5′-UTR	3804	6.91	16.10	32.20	3601	7.30	16.19	32.60	1335	19.69	16.23	26.55
3′-UTR	3829	6.87	16.13	33.68	3628	7.25	16.22	33.94	1341	19.62	15.90	26.70
CDS	2553	17.27	19.80	74.82	2391	23.10	19.87	75.28	309	178.73	21.28	56.84
Intron	11 857	10.13	16.03	29.94	11 038	10.88	16.12	29.97	4704	25.54	16.70	29.60
Promotors	10 370	6.26	17.35	27.57	9248	7.02	17.54	26.71	3344	19.42	17.26	20.82
Intergenic	107 658	21.63	16.17	50.49	65 098	28.56	17.12	46.22	21 650	85.88	17.70	42.24
Total/average	136 039	15.15	16.33	47.01	90 441	22.79	17.11	42.62	30 900	66.70	17.49	37.61
Z. Mexicana
5′-UTR	2520	10.25	15.55	26.23	2263	11.42	15.66	24.10	1007	25.66	14.35	17.18
3′-UTR	3329	7.76	17.34	38.34	3092	8.35	17.42	38.10	1100	23.48	15.81	23.81
CDS	3636	14.29	17.70	45.01	3252	15.98	17.93	43.96	954	54.47	16.14	23.08
Intron	8102	14.23	16.24	32.41	7168	16.08	16.48	30.43	3035	37.98	15.63	24.71
Promotors	10 903	5.86	17.79	34.35	10 035	6.37	17.95	34.04	3627	17.62	16.32	21.71
Intergenic	107 785	16.50	16.18	49.95	57 813	30.76	17.51	42.07	22 413	79.33	16.64	38.84
Total/average	133 346	15.46	16.38	47.13	80 545	25.59	17.50	39.82	30 787	66.94	16.45	34.45
P1
5′-UTR	2684	9.60	15.27	24.75	2419	10.65	15.37	22.50	926	27.82	15.44	20.02
3’-UTR	3478	7.41	17.04	37.07	3230	7.98	17.11	36.90	1044	24.68	16.96	29.53
CDS	3724	13.91	17.44	44.49	3351	15.46	17.63	43.48	911	56.86	17.51	28.36
Intron	8622	13.32	15.96	31.18	7659	14.99	16.14	29.13	3073	37.36	16.28	28.44
Promotors	11 218	5.68	17.56	33.82	10 316	6.18	17.67	33.50	3486	18.28	17.56	24.74
Intergenic	110 043	16.17	16.06	49.51	59 167	30.07	17.26	41.81	22 475	79.16	17.39	41.03
Total/average	136 613	15.09	16.24	46.58	82 831	24.88	17.24	39.38	30 621	67.31	17.28	37.09