Table 2. Occurrence and distribution of repetitive DNA in the maize BAC end sequences.

Class, subclass, group, clade	No. of hits	Percentage of hits, %	No. of bases, bp	Percentage of masked bases, %	Percentage of genome,* %
Class I elements (retroelements)		92.65		96.01	55.60
LTR-retrotransposons		90.91		95.65	55.38
Ty1/copia-like elements	133,860	39.74		42.37	24.54
Ji	71,923	21.35	42,306,471	23.78	13.77
Opie	37,451	11.12	22,168,294	12.46	7.22
Prem	14,129	4.19	6,439,116	3.62	2.10
Other copia	10,357	3.07	4,455,318	2.50	1.45
Ty3/gypsy-like elements	116,375	34.55		37.02	21.43
Cinful	40,706	12.08	24,989,484	14.05	8.14
Grande	16,752	4.97	9,772,902	5.49	3.18
Huck	16,892	5.01	9,107,710	5.12	2.97
Tekay	3,116	0.93	1,472,939	0.83	0.48
Zeon	30,305	9.00	17,452,971	9.81	5.68
Other gypsy	8,604	2.55	3,043,159	1.71	0.99
Other LTR-retrotransposons	55,941	16.61	28,912,679	16.25	9.41
Retroposons without LTR		1.75		0.36	0.21
LINEs	1,237	0.37	285,530	0.16	0.09
SINEs	3,802	1.13	256,122	0.14	0.08
Other unclassified retroelements	847	0.25	104,778	0.06	0.03
Class II elements (DNA transposons)		4.12		1.69	0.98
hAT superfamily (hobo-Ac-Tam3)	4,310	0.15	84,656	0.05	0.03
CATA superfamily (En/Spm)	3,140	0.93	981,562	0.55	0.32
MuDR/Mu superfamily	502	0.15	42,734	0.02	0.01
MITEs		1.28	523,368	0.29	0.17
Helitrons	144	0.04	11,174	0.01	0.00
Other unclassified DNA transposons	5,274	1.57	1,366,349	0.77	0.44
Simple repeats		1.42		0.68	0.40
Centromeric repeats	2,348	0.70	598,640	0.34	0.19
Telomeric repeats	465	0.14	131,884	0.07	0.04
VNTR (mini- and microsatellites)	1,030	0.31	85,500	0.05	0.03
Knob-region	956	0.28	402,235	0.23	0.13
High-copy-number genes (ribosomal)	4,908	1.46	2,506,369	1.41	0.82
Other undefined repeats	1,179	0.35	364,729	0.21	0.12
Total	336,840	100	177,871,282	100	57.91

Greater than 70% identity limit. MITE, miniature inverted-repeat TE; LINE, long interspersed nuclear element; SINE, short interspersed nuclear element; VNTR, variable number terminal repeat.

^*Based on 2,365 Mb.