Characteristics of Rice Microsatellites and Efficiency of SSR Marker Development
| Class of microsatellite markers | No. primer pairs ordered[i] | Mean no.repeats in SSR[ii] | Mean GC% in flanking regions[iii] | Rate of successful amplification | Percent of polymorphic SSRs | No. mapped markers |
| GA | 130 | 15.0 | 44 | 83.8% | 80.7 | 88 |
| CA | 32 | 12.1 | 38 | 71.8% | 73.9 | 17 |
| AT | 63 | 22.3 | 39 | 31.7% | 80.0 | 16 |
| GC-rich TNRs | 45 | 7.8 | 54 | 64.4% | 65.5 | 18 |
| ATT | 23 | 17.6 | 36 | 78.3% | 72.2 | 13 |
| GAA | 23 | 12.7 | 47 | 87.0% | 80.0 | 16 |
| CAT and CAA | 12 | 8.8 | 50 | 83.3% | 70.0 | 7 |
| Tetranucleotides | 42 | 6.1 | 41 | 71.4% | 60.0 | 18 |
| (TA)n(CA)n | 12 | 39.8 | 39 | 58.3% | 100 | 7 |
| TOTAL | 382 | 200 |
[i] The number includes 362 primer pairs ordered for BAC-end derived SSRs and 20 markers selected from the fully-sequenced BACs and PACs.
[ii] The mean number of repeats was calculated for the sequences selected for the primer design.
[iii] The mean GC content in flanking regions was estimated based on a total number of sequences in this class analyzed in this study.