Table 3.

Association between Rice Microsatellites and Other Types of Repetitive Elements in BAC-end Sequences

	Number of sequences in this class
Type of homology		*BAC ends from the HindIII library*		*BAC ends from EcoRI library*
		(AT)n		(CA)n		(AT)n		(CA)n
		no.	%	no.	%	no.	%	no.	%
>80% with Micropon-4	3	1.0	0		47	29.7	0
>80% with other Micropons	0		0		4	2.5	2	5.5
54%–80% with any Micropons	40	13.1	10	15.4	26	16.5	9	25.0
>80% with non-Micropon MITEs	11	3.6	2	3.1	0		0
54%–80% with non-Micropon MITEs	29	9.5	11	16.9	23	14.6	11	30.6
Any retroelement homology	13	4.3	5	7.7	5	3.2	1	2.8
Other (centromeric, ribosomal, etc.)	18	5.9	2	3.1	3	1.9	0
Unique, no homology with any repeats in TIGR database on either end of SSR	188	61.6	35	53.8	50	31.6	13	36.1
TOTAL	304		65		158		36

↵54%–70% similarities have been confirmed to be genuine by the length and/or complexity of the homology. The original sequences of the Micropon elements are available as GenBank accession nos. AB010111–AB010115.

Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential