Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus

Table 1 Number and distribution of SSRs in consensus EST and transcript sequences.

	Organism
	P. infestans	P. sojae	P. ramorum
Total number of sequences examined	25965	19276	16066
Total size covered by examined sequences (Mb)	12.573	29.249	22.097
Total number of SSRs identified	1660	5938	2838
Perfect ^a	1466 (88.31 %)	4859 (81.83 %)	2554 (89.99 %)
Within a compound formation ^b	194 (11.69 %)	1079 (18.17%)	284 (10.01 %)
Number of SSR-containing sequences:	1466 (5.65 %)	4265 (22.13 %)	2320 (14.44 %)
Number of sequences containing more than one SSR	152 (0.59 %)	1142 (5.92 %)	377 (2.35 %)
Total relative abundance (SSRs/Mb)	132.02	203.01	128.43
Total relative density (bp/Mb)	1803.66	2819.08	1723.24

Analysis was based on the MISA script, which identified di- to hexa-nucleotide repeat motifs (perfect and compound microsatellites) that are at least 12 bases in length.
^a Perfect microsatellites consist of a single repeat motif and are not interrupted anywhere by a base that does not fit the repeat structure
^b Compound microsatellites consist of two or more adjacent microsatellites with different repeat types