Table 2.

Classification and distribution of known plant repeats in the BAC end sequences

	Tom. HBa	Tom. Eco	Tom. Mbo	Pot. POT	Pot. PPT
Class I retrotransposons	16.95	9.30	13.81	11.42	8.19
LTR retrotransposons	16.81	9.19	13.72	11.16	7.92
Ty1/Copia	5.25	4.17	4.39	2.55	2.48
Ty3/Gypsy	11.56	5.02	9.33	8.60	5.43
Unclassified	0.00	0.00	0.00	0.01	0.01
Non-LTR retrotransposons	0.14	0.11	0.09	0.26	0.27
LINE	0.09	0.06	0.05	0.15	0.13
SINE	0.05	0.05	0.04	0.11	0.14
Class II DNA transposons	0.64	0.66	0.49	1.03	1.23
En-Spm	0.26	0.26	0.21	0.27	0.27
Harbinger	0.00	0.00	0.00	0.00	0.00
Mariner	0.00	0.00	0.00	0.00	0.00
MuDR	0.07	0.09	0.05	0.10	0.11
Pogo	0.02	0.03	0.02	0.03	0.08
Stowaway	0.02	0.02	0.02	0.01	0.02
TcMar-Stowaway	x	x	x	0.00	0.00
Tourist	x	x	0.00	0.00	x
hAT	0.02	0.04	0.02	0.05	0.19
hAT-Ac	0.01	0.00	0.01	0.01	0.01
hAT-Tip100	0.02	0.02	0.02	0.11	0.10
Unclassified	0.22	0.20	0.14	0.45	0.45
Satellites	0.00	0.00	0.00	0.04	0.03
Centromeric	0.00	x	0.00	0.00	0.00
Subtelomeric	x	x	x	0.00	0.00
Unclassified	0.00	0.00	0.00	0.04	0.03
Ribosomal genes	0.04	2.98	8.58	0.03	0.53
rRNA	0.04	2.98	8.58	0.03	0.53
Unclassified	0.08	0.11	0.07	0.07	0.11
Centromeric	x	x	x	0.00	x
Composite	x	x	x	x	0.00
RC/Helitron	0.08	0.11	0.07	0.06	0.11
Unknown	0.00	0.00	0.00	0.01	0.00
Total	17.66	13.01	22.91	12.54	10.02

Numbers represent percentages of nucleotides that show similarity to a repeat of the indicated category. An 'x' represents the absence of a repeat family; '0.00' indicates that the repeat is present, but at a frequency lower than 0.005 % of the nucleotides in the BESs. Species names have been abbreviated as follows: Tom.: tomato; Pot.: potato.