Table 1.

BLAST Results of Small Insert Maize Library “cne1g”

Category	Homology	# of sequences	% of total	95% C.I.	Element type	Size of element (LTR)
Retroelement-related sequences	Ji	203	9.4	8.25–10.71	copia	8.3 kb (1.1 kb)
	Opie	154	7.1	6.13–8.30	copia	9.0 kb (1.1 kb)
	Prem-2	35	1.6	1.17–2.25	copia	9.4 kb (1.3 kb)
	Victim	4	0.2	0.00–0.42	copia	5.4 kb (100 bp)
	Fourf	8	0.4	0.09–0.70	copia	6.8 kb (1.1 kb)
	Hopscotch	1	0.0	0.00–0.19	copia	4.8 kb (230 bp)
	Huck	231	10.7	9.47–12.08	gypsy	11–12 kb (1.61 kb)
	Grande1–4	85	3.9	3.20–4.85	gypsy	13.7 kb (600 bp)
	Cinful	76	3.5	2.82–4.39	gypsy	8.5 kb (600 bp)
	‘ANLI’ retro	67	3.1	2.45–3.93	gypsy	Unknown
	Tekay	26	1.2	0.82–1.76	gypsy	12 kb (3.2 kb)
	Milt	15	0.7	0.42–1.14	gypsy	4.7 kb (700 bp)
	Reina	0	0.0	0.00–0.14	gypsy	5.4 kb (300 bp)
	Magellan	0	0.0	0.00–0.14	gypsy	5.7 kb (340 bp)
	Zeon-1	103	4.8	3.95–5.76	—	7.3 kb (650 bp)
	Prem-1	53	2.5	1.88–3.20	LTR only	Unknown (1–1.6)
	Cin1	11	0.5	0.19–0.84	LTR only	Unknown (700 bp)
	Kake	4	0.2	0.00–0.42	—	5.9 kb (170 bp)
	Other retrotransposons	151	7.0	6.00–8.16	—
	LINEs	3	0.1	0.00–0.37
Unknown repeats	Repeat–22kD zein region	92	4.3	3.49–5.20
	Repeat–19 kD zein region	16	0.7	0.46–1.20
	Repeat–unknown	196	9.1	7.95–10.37
Other dispersed repeats	DNA transposons	26	1.2	0.82–1.76
Other dispersed repeats	MITEs	15	0.7	0.42–1.14
Tandemly repetitive sequences	Knob repeats	42	1.9	1.44–2.62
	Ribosomal DNA	39	1.8	1.33–2.46
	Centromeric repeats	10	0.5	0.14–0.79
Other	Chloroplast DNA	37	1.7	1.25–2.36
	Similarity to genes	117	5.4	4.55–6.46
	Unknown	337	15.6	14.15–17.22

↵C.I., 95% confidence interval for estimate of the percentage of the genome comprised by each class.
↵The size of the known retroelements and LTRs was determined from GenBank accessions.

Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome