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Table 3 Motif length and position of polymorphic SSRs in EST sequences of chicken, rice, Arabidopsis, Brassica, potato and tomato

From: Large-scale identification of polymorphic microsatellites using an in silico approach

species   Dia- Tri-a Pentaa Othersb total Densityc
chicken all 846 (49%) 378 (22%) 386 (22%) 114 (7%) 1724 (100%) 71.51
  coding 95 70 38 9 212 55.13
  5'UTR1 19 33 24 10 86 137.66
  3'UTR2 155 54 77 24 310 74.81
  TSS3 1 3 3 1 8  
rice all 1070 (40%) 1113 (42%) 320 (12%) 143 (5%) 2646 (100%) 93.47
  coding 154 372 86 26 638 57.33
  5'UTR1 294 285 69 32 680 227.16
  3'UTR2 342 121 70 36 569 92.66
  TSS3 5 0 1 1 7  
Arabidopsis all 668 (53%) 410 (33%) 133(11%) 37 (3%) 1248 (100%) 102.63
  coding 196 222 34 13 465 72.84
  5'UTR1 193 73 34 7 307 215.96
  3'UTR2 136 42 40 10 228 112.02
  TSS3 6 2 1 1 10  
Brassica all 468 (47%) 350 (35%) 139 (14%) 40 (4%) 997 (100%) 119.45
  coding 55 203 43 13 314 63.09
  5'UTR1 205 55 27 13 300 378.62
  3'UTR2 126 44 47 9 226 169.90
  TSS3 1 2 3 2 8  
potato all 379 (35%) 358 (33%) 248 (23%) 95 (9%) 1080 (100%) 89.78
  coding 61 155 87 44 347 62.66
  5'UTR1 64 38 29 8 139 160.21
  3'UTR2 129 40 59 24 252 134.75
  TSS3 0 1 3 1 5  
tomato all 124 (47%) 79 (30%) 54 (20%) 8 (3%) 265 (100%) 98.52
  coding 42 35 19 2 98 67.06
  5'UTR1 50 18 19 1 88 265.74
  3'UTR2 12 7 5 0 24 70.79
  TSS3 1 1 1 1 4  
  1. aDi- is dinucleotide SSR, and so on for others; bothers means tetranucleotide and hexanucleotides repeats or higher
  2. cDensity of number of SSR per 100 kb of EST sequences (See Materials & Methods).
  3. 1 5' UTR is the portion of an mRNA from the 5' end to the position of the first codon used in translation.
  4. 2The 3' UTR is the portion of an mRNA from the last codon used in translation to the 3' end of the mRNA.
  5. 3 TSS is the position of the first codon (translation start) and the last codon (translation stop) used in translation. SSR contain the first codon or the last codon.