A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens

BMC Genomics

Table 6 The SSR frequency and distribution in the UV-8b BESs

Type (motif number)¹	Average length (bp)	SSR number	Counts/Mb	Read number²	Primer number³
Mononucleotide (2)	22.68	339	124.64	329	248
A	23.76	268	98.53	258	204
C	18.59	71	26.10	71	44
Dinucleotide (3)	29.40	57	20.96	57	44
AG	28.48	33	12.13	33	23
AT	30.27	15	5.51	15	14
AC	31.33	9	3.31	9	7
Trinucleotide (10)	27.16	223	81.99	215	191
AGC	29.98	42	15.44	37	37
AAG	31.63	40	14.71	38	33
ACG	27.00	36	13.24	36	32
CCG	22.40	30	11.03	30	27
AAT	17.75	16	5.88	16	13
ATC	31.38	16	5.88	16	13
others	25.33	43	15.81	42	36
Tetranucleotide (23)	25.14	113	41.55	113	100
AAAG	25.46	13	4.78	13	12
AGGC	24.92	12	4.41	12	10
ACCT	23.27	11	4.04	11	11
AGCC	30.33	9	3.31	9	6
others	25.84	68	25.01	68	61
Pentanucleotide (53)	22.72	158	58.09	155	137
AAAAG	25.82	22	8.09	20	15
AAAAT	21.06	16	5.88	16	14
ACCAG	27.00	10	3.68	10	10
others	22.02	110	40.44	109	98
Hexanucleotide (85)	29.28	133	48.90	133	116
AAAAAG	33.67	6	2.21	6	5
AGCGGC	24.00	5	1.84	5	4
ATATCG	20.40	5	1.84	5	5
others	32.13	117	43.01	117	102
Total	25.17	1023	376.12	849	836

¹Group all the similar and reverse complementary SSR motifs together, e.g. “TC”, “CT”, “AG”, and “GA” were grouped into “AG”.
²The number of sequence reads that contain SSRs.
³The primer numbers that were successfully designed for SSR loci.

ISSN: 1471-2164