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Table 2 SSR motifs and their frequency in 3′ UTR, 5′ UTR and coding regions

From: A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica

   Estimated location  
SSR motif 3' UTR 5' UTR coding undetermined Total
di AT 154 70 73 6 303
  AG 42 53 155 6 256
  AC 27 18 46 3 94
  CG 0 0 2 0 2
  sub-total 223 141 276 15 655
tri AAG 19 36 285 2 342
  ATG 19 32 178 1 230
  AGG 7 49 170 0 226
  AGC 18 34 129 2 183
  AAT 55 22 49 2 128
  ACC 6 7 64 0 77
  GGC 9 15 38 0 62
  AAC 11 9 32 0 52
  ACG 0 1 11 0 12
  AGT 2 1 4 0 7
  sub-total 146 206 960 7 1319
tetra   61 65 60 8 194
penta   180 193 349 19 741
hexa   154 225 703 12 1094
compound   15 5 35 1 56
  Total   779 835 2383 62 4059
  1. SSR location was estimated by inferring coding regions using the prot4EST pipeline [44] and the fasty35 module of the FASTA package [49]. Some of the locations were un-determined because the corresponding SSRs extended over both coding and non-coding regions.