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

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

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