Resource Review
SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation
Table 2
Distribution of SSR/minisatellite repeats in the rice cDNA collection.
| | Motif | | Ocur(1) | (%)(1) | Ocur(2) | (%)(2) | Total | (%) Group | (%) Overall |
| | Mono- | A/T | 111 | 88.80 | 14 | 11.20 | 125 | 90.58 | 3.20 | | C/G | 10 | 76.92 | 3 | 23.08 | 13 | 9.42 | 0.33 |
| | 2-mer | AG/CT | 97 | 36.06 | 172 | 63.94 | 269 | 45.29 | 6.89 | | GA/TC | 143 | 61.37 | 90 | 38.63 | 233 | 39.23 | 5.96 | | CA/TG | 10 | 35.71 | 18 | 64.29 | 28 | 4.71 | 0.72 | | AT | 24 | 100.00 | — | — | 24 | 4.04 | 0.61 | | AC/GT | 6 | 31.58 | 13 | 68.42 | 19 | 3.20 | 0.49 | | TA | 19 | 100.00 | — | — | 19 | 3.20 | 0.49 | | CG | 2 | 100.00 | — | — | 2 | 0.34 | 0.05 |
| | 3-mer | CCG/CGG | 197 | 53.68 | 170 | 46.32 | 367 | 18.44 | 9.39 | | CGC/GCG | 218 | 61.24 | 138 | 38.76 | 356 | 17.89 | 9.11 | | GCC/GGC | 112 | 53.08 | 99 | 46.92 | 211 | 10.60 | 5.40 | | CTC/GAG | 73 | 42.69 | 98 | 57.31 | 171 | 8.59 | 4.38 | | AGG/CCT | 34 | 30.91 | 76 | 69.09 | 110 | 5.53 | 2.82 | | GGA/TCC | 60 | 62.50 | 36 | 37.50 | 96 | 4.82 | 2.46 | | CAG/CTG | 58 | 76.32 | 18 | 23.68 | 76 | 3.82 | 1.95 | | AAG/CTT | 34 | 50.75 | 33 | 49.25 | 67 | 3.37 | 1.71 | | CGA/TCG | 33 | 54.10 | 28 | 45.90 | 61 | 3.07 | 1.56 | | AGC/GCT | 36 | 62.07 | 22 | 37.93 | 58 | 2.91 | 1.48 | | GCA/TGC | 47 | 83.93 | 9 | 16.07 | 56 | 2.81 | 1.43 | | AGA/TCT | 33 | 62.26 | 20 | 37.74 | 53 | 2.66 | 1.36 | | CCA/TGG | 39 | 75.00 | 13 | 25.00 | 52 | 2.61 | 1.33 | | ACC/GGT | 22 | 48.89 | 23 | 51.11 | 45 | 2.26 | 1.15 | | GAA/TTC | 28 | 63.64 | 16 | 36.36 | 44 | 2.21 | 1.13 | | CAC/GTG | 28 | 65.12 | 15 | 34.88 | 43 | 2.16 | 1.10 | | GAC/GTC | 18 | 54.55 | 15 | 45.45 | 33 | 1.66 | 0.84 | | ACG/CGT | 11 | 42.31 | 15 | 57.69 | 26 | 1.31 | 0.67 | | ATC/GAT | 5 | 45.45 | 6 | 54.55 | 11 | 0.55 | 0.28 | | TCA/TGA | 5 | 50.00 | 5 | 50.00 | 10 | 0.50 | 0.26 | | CAA/TTG | 4 | 50.00 | 4 | 50.00 | 8 | 0.40 | 0.20 | | ACT/AGT | 3 | 42.86 | 4 | 57.14 | 7 | 0.35 | 0.18 | | TAA/TTA | 1 | 14.29 | 6 | 85.71 | 7 | 0.35 | 0.18 | | CTA/TAG | 4 | 66.67 | 2 | 33.33 | 6 | 0.30 | 0.15 | | AAT/ATT | 1 | 20.00 | 4 | 80.00 | 5 | 0.25 | 0.13 | | CAT/ATG | 4 | 100.00 | 0 | 0 | 4 | 0.20 | 0.10 | | AAC/GTT | 3 | 75.00 | 1 | 25.00 | 4 | 0.20 | 0.10 | | ATA/TAT | 1 | 50.00 | 1 | 50.00 | 2 | 0.10 | 0.05 | | GTA/TAC | 1 | 100.00 | 0 | 0 | 1 | 0.05 | 0.03 |
| | 4-mer | GATC | 18 | 100.00 | 0 | 0 | 18 | 7.17 | 0.46 | | ATTA/TAAT | 9 | 52.94 | 8 | 47.06 | 17 | 6.77 | 0.44 | | ATCG/CGAT | 3 | 20.00 | 12 | 80.00 | 15 | 5.98 | 0.38 | | CATC/GATG | 4 | 40.00 | 6 | 60.00 | 10 | 3.98 | 0.26 | | AGAA/TTCT | 2 | 25.00 | 6 | 75.00 | 8 | 3.19 | 0.20 | | GCTA/TAGC | 6 | 75.00 | 2 | 25.00 | 8 | 3.19 | 0.20 | | GATA/TATC | 1 | 14.29 | 6 | 85.71 | 7 | 2.79 | 0.18 | | GCGA/TCGC | 3 | 42.86 | 4 | 57.14 | 7 | 2.79 | 0.18 | | GCAC/GTGC | 2 | 33.33 | 4 | 66.67 | 6 | 2.39 | 0.15 | | AGGG/CCCT | 2 | 33.33 | 4 | 66.67 | 6 | 2.39 | 0.15 |
| | 5-mer | AGGAG/CTCCT | 3 | 15.00 | 17 | 85.00 | 20 | 4.69 | 0.51 | | CTCTC/GAGAG | 17 | 89.47 | 2 | 10.53 | 19 | 4.46 | 0.49 | | GAGGA/TCCTC | 9 | 56.25 | 7 | 43.75 | 16 | 3.76 | 0.41 | | CCTCC/GGAGG | 12 | 80.00 | 3 | 20.00 | 15 | 3.52 | 0.38 | | AGAGG/CCTCT | 4 | 26.67 | 11 | 73.33 | 15 | 3.52 | 0.38 | | GGAGA/TCTCC | 2 | 18.18 | 9 | 81.82 | 11 | 2.58 | 0.28 | | CTCGC/GCGAG | 7 | 77.78 | 2 | 22.22 | 9 | 2.11 | 0.23 | | AGCTA/TAGCT | 4 | 44.44 | 5 | 55.56 | 9 | 2.11 | 0.23 | | GAAAA/TTTTC | 2 | 25.00 | 6 | 75.00 | 8 | 1.88 | 0.20 | | AGGCG/CGCCT | 2 | 25.00 | 6 | 75.00 | 8 | 1.88 | 0.20 |
| | 6-mer | CGCCTC/GAGGCG | 12 | 85.71 | 2 | 14.29 | 14 | 3.59 | 0.36 | | CGGCGA/TCGCCG | 4 | 28.57 | 10 | 71.43 | 14 | 3.59 | 0.36 | | CCTCCG/CGGAGG | 9 | 81.82 | 2 | 18.18 | 11 | 2.82 | 0.28 | | AGGCGG/CCGCCT | 1 | 10.00 | 9 | 90.00 | 10 | 2.56 | 0.26 | | CCGTCG/CGACGG | 4 | 44.44 | 5 | 55.56 | 9 | 2.31 | 0.23 | | CGTCGC/GCGACG | 7 | 77.78 | 2 | 22.22 | 9 | 2.31 | 0.23 | | ACCGCC/GGCGGT | 1 | 12.50 | 7 | 87.50 | 8 | 2.05 | 0.20 | | CCACCG/CGGTGG | 6 | 85.71 | 1 | 14.29 | 7 | 1.79 | 0.18 | | GGCGGA/TCCGCC | 5 | 71.43 | 2 | 28.57 | 7 | 1.79 | 0.18 | | CTCCAT/ATGGAG | 6 | 100.00 | 0 | 0 | 6 | 1.54 | 0.15 |
| | 7-mer | CCGCCGC/GCGGCGG | 4 | 66.67 | 2 | 33.33 | 6 | 7.32 | 0.15 | | CTCTCTC/GAGAGAG | 4 | 80.00 | 1 | 20.00 | 5 | 6.10 | 0.13 | | CCTCTCT/AGAGAGG | 4 | 100.00 | 0 | 0 | 4 | 4.88 | 0.10 | | CTCTCTT/AAGAGAG | 4 | 100.00 | 0 | 0 | 4 | 4.88 | 0.10 | | CCCAAAT/ATTTGGG | 3 | 100.00 | 0 | 0 | 3 | 3.66 | 0.08 | | GCCGCCG/CGGCGGC | 3 | 100.00 | 0 | 0 | 3 | 3.66 | 0.08 | | GCGGCGC/GCGCCGC | 2 | 100.00 | 0 | 0 | 2 | 2.44 | 0.05 | | AATAAAA/TTTTATT | 2 | 100.00 | 0 | 0 | 2 | 2.44 | 0.05 | | GTGTGCG/CGCACAC | 2 | 100.00 | 0 | 0 | 2 | 2.44 | 0.05 | | CGCCGTC/GACGGCG | 2 | 100.00 | 0 | 0 | 2 | 2.44 | 0.05 |
| | 8-mer | TTGGTTTC/GAAACCAA | 2 | 100.00 | 0 | 0 | 2 | 33.33 | 0.05 | | TGGGCTTG/CAAGCCCA | 1 | 100.00 | 0 | 0 | 1 | 16.67 | 0.03 | | GCTTCTTG/CAAGAAGC | 1 | 100.00 | 0 | 0 | 1 | 16.67 | 0.03 | | ACGGGCGA/TCGCCCGT | 1 | 100.00 | 0 | 0 | 1 | 16.67 | 0.03 | | ATGATGTA/TACATCAT | 1 | 100.00 | 0 | 0 | 1 | 16.67 | 0.03 |
| | 9-mer | TCGGCGGCG/CGCCGCCGA | 2 | 100.00 | 0 | 0 | 2 | 8.00 | 0.05 | | AGGTGGTGG/CCACCACCT | 2 | 100.00 | 0 | 0 | 2 | 8.00 | 0.05 | | CCGGTGCGA/TCGCACCGG | 1 | 100.00 | 0 | 0 | 1 | 4.00 | 0.03 | | ACGAGGAGG/CCTCCTCGT | 1 | 100.00 | 0 | 0 | 1 | 4.00 | 0.03 | | TCCCTTTTC/GAAAAGGGA | 1 | 100.00 | 0 | 0 | 1 | 4.00 | 0.03 | | CGGCATGAA/TTCATGCCG | 1 | 100.00 | 0 | 0 | 1 | 4.00 | 0.03 | | CGGCAGCGA/TCGCTGCCG | 1 | 100.00 | 0 | 0 | 1 | 4.00 | 0.03 | | ACCATCCCG/CGGGATGGT | 1 | 100.00 | 0 | 0 | 1 | 4.00 | 0.03 | | ATGGGCGGC/GCCGCCCAT | 1 | 100.00 | 0 | 0 | 1 | 4.00 | 0.03 | | ATGCAGGGT/ACCCTGCAT | 1 | 100.00 | 0 | 0 | 1 | 4.00 | 0.03 |
| | 10-mer | AGCCCCAACG/CGTTGGGGCT | 1 | 50.00 | 1 | 50.00 | 2 | 40.00 | 0.05 | | TTTTTTTCTT/AAGAAAAAAA | 1 | 100.00 | 0 | 0 | 1 | 20.00 | 0.03 | | CCTGCTTTGC/GCAAAGCAGG | 1 | 100 | 0 | 0 | 1 | 20 | 0.03 | | ATCTCCGCCG/CGGCGGAGAT | 1 | 100 | 0 | 0 | 1 | 20 | 0.03 |
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