Table 1 Number of intermediate EST results at each ESAP Plus major stage
From: ESAP plus: a web-based server for EST-SSR marker development
Number of raw ESTs | 232352 | |||
|---|---|---|---|---|
Step 1. Pre-processing | ||||
 N > 5% | 1322 | |||
 Vector trimming | 42594 | |||
 Vector-contaminated deletion | 62 | |||
 Low-complexity masking | 5194 | |||
 Number of high-quality ESTs | 226078 | |||
Step 2. Clustering and assembly | ||||
 Software options | CD-HIT-EST | TGICL | ||
 Number of NR clusters/ASs | 142788 | 65713 | ||
 Total length (bp) | 95445342 | 51256243 | ||
Step 3. SSR identification | ||||
 Software options | MISA | RepeatMasker | MISA | RepeatMasker |
 Number of SSR containing in NR clusters/ASs | 9327 | 25708 | 5412 | 14490 |
 Total number of identified SSRs | 10240 | 32021 | 5951 | 18526 |
Number of SSR types | ||||
 di-NTRs | 2446 | 1784 | 1203 | 884 |
 tri-NTRs | 7311 | 15410 | 4446 | 9291 |
 tetra-NTRs | 247 | 2419 | 159 | 1341 |
 penta-NTRs | 128 | 2524 | 77 | 1355 |
 hexa-NTRs | 108 | 9884 | 66 | 5655 |
 An average of 1 SSR/Kbp | 9.32 | 2.98 | 8.61 | 2.77 |
Step 4. Primer design | ||||
 Number of successfully designed SSR primer pairs | 7850 | 6272 | 4613 | 3783 |