| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16-trnQ-UUG | LSC | 1060 | 0.0272 | 0.99 | 65.3 | yes | View details |
| trnfM-CAU-trnT-GGU | LSC | 2375 | 0.0163 | 1.00 | 56.1 | yes | View details |
| trnY-GUA-trnD-GUC | LSC | 363 | 0.0317 | 0.99 | 65.0 | yes | View details |
| trnD-GUC-psbM | LSC | 380 | 0.0237 | 1.00 | 57.6 | yes | View details |
| psbM-petN | LSC | 763 | 0.0240 | 0.97 | 67.8 | yes | View details |
| rpoC2 | LSC | 4542 | 0.0108 | 1.00 | 44.6 | yes | View details |
| rbcL-accD | LSC | 1026 | 0.0200 | 1.00 | 59.7 | yes | View details |
| psaJ-rpl33 | LSC | 462 | 0.0183 | 1.00 | 48.9 | yes | View details |
| ndhF-rpl32 | SSC | 751 | 0.0193 | 0.95 | 62.4 | yes | View details |
| petA-psbJ | LSC | 996 | 0.0177 | 1.00 | 62.9 | yes | View details |
| atpI-atpH | LSC | 826 | 0.0103 | 0.96 | 57.3 | yes | View details |
| rpl32-trnL-UAG | SSC | 541 | 0.0194 | 1.00 | 56.6 | yes | View details |
| ndhC-trnV-UAC | LSC | 790 | 0.0168 | 1.00 | 55.7 | yes | View details |
| trnG-UCC-trnfM-CAU | LSC | 433 | 0.0169 | 1.00 | 54.1 | yes | View details |
| atpB-rbcL | LSC | 803 | 0.0123 | 0.99 | 54.0 | yes | View details |
| rps19-psbA | LSC | 127 | 0.0216 | 0.98 | 53.8 | no | View details |
| trnC-GCA-rpoB | LSC | 1105 | 0.0135 | 1.00 | 52.8 | yes | View details |
| trnT-GGU-trnE-UUC | LSC | 523 | 0.0185 | 0.99 | 52.2 | yes | View details |
| Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped. | |||||||
Species
22
Genome length
134–136 kb
Candidate markers
269
Primer pairs
85
Genome-wide nucleotide diversity
Candidate markers
9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).
Primer pairs
Showing the top 30 of 85 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | CCACAATCGATCGTGTCCTT |
GAGGTTCGAATCCTTCCGTC |
698–1156 | 1.000 | 91.2 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | CCACAATCGATCGTGTCCTT |
TGACAGGCATAACATCCACG |
1218–1676 | 1.000 | 89.9 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | CCACAATCGATCGTGTCCTT |
CTTACAGCAGCTTGCCAAAC |
1267–1725 | 1.000 | 89.4 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | TGGTGGGTAGCAAAATCCAC |
TGACAGGCATAACATCCACG |
1234–1692 | 1.000 | 89.3 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TGGTGGGTAGCAAAATCCAC |
CTTACAGCAGCTTGCCAAAC |
1283–1741 | 1.000 | 88.8 |
| trnG-UCC-trnfM-CAU_p1 | trnG-UCC-trnfM-CAU | GCGAGCGTAGTTCAATGGTA |
CGAGGCTCATAACCTTGAGG |
483–555 | 1.000 | 85.5 |
| trnG-UCC-trnfM-CAU_p2 | trnG-UCC-trnfM-CAU | GCGAGCGTAGTTCAATGGTA |
CAGTTTGGTAGCTCACGAGG |
498–570 | 1.000 | 84.9 |
| trnG-UCC-trnfM-CAU_p3 | trnG-UCC-trnfM-CAU | CGTAGCGAGCGTAGTTCAAT |
CGAGGCTCATAACCTTGAGG |
487–559 | 1.000 | 84.7 |
| trnG-UCC-trnfM-CAU_p4 | trnG-UCC-trnfM-CAU | ATATAGGACGTAGCGAGCGT |
CGAGGCTCATAACCTTGAGG |
495–567 | 1.000 | 84.6 |
| trnG-UCC-trnfM-CAU_p5 | trnG-UCC-trnfM-CAU | CCCAGGCGGATATACCCTAT |
CGAGGCTCATAACCTTGAGG |
530–590 | 0.909 | 81.1 |
| trnfM-CAU-trnT-GGU_p1 | trnfM-CAU-trnT-GGU | CCTCAAGGTTATGAGCCTCG |
CCACTGAGTTAAAAGGGC |
2210–2474 | 1.000 | 48.3 |
| trnfM-CAU-trnT-GGU_p2 | trnfM-CAU-trnT-GGU | CCTCGTGAGCTACCAAACTG |
CCACTGAGTTAAAAGGGC |
2195–2459 | 1.000 | 48.3 |
| trnfM-CAU-trnT-GGU_p3 | trnfM-CAU-trnT-GGU | CAAGGTTATGAGCCTCGTGA |
CCACTGAGTTAAAAGGGC |
2207–2471 | 1.000 | 48.3 |
| trnfM-CAU-trnT-GGU_p4 | trnfM-CAU-trnT-GGU | TCAAGGTTATGAGCCTCGTG |
CCACTGAGTTAAAAGGGC |
2208–2472 | 1.000 | 48.3 |
| trnfM-CAU-trnT-GGU_p5 | trnfM-CAU-trnT-GGU | TATGAGCCTCGTGAGCTACC |
CCACTGAGTTAAAAGGGC |
2201–2465 | 1.000 | 48.3 |
| trnT-GGU-trnE-UUC_p1 | trnT-GGU-trnE-UUC | AGGCATAAGTCATCGGTTCA |
TGTCCTGAACCACTAGACGA |
579–592 | 1.000 | 73.8 |
| trnT-GGU-trnE-UUC_p2 | trnT-GGU-trnE-UUC | AGGCATAAGTCATCGGTTCA |
GCTGCCTCCTTGAAAGAGAG |
600–613 | 1.000 | 73.7 |
| trnT-GGU-trnE-UUC_p3 | trnT-GGU-trnE-UUC | TGGTAAGGCATAAGTCATCGG |
TGTCCTGAACCACTAGACGA |
584–597 | 1.000 | 72.9 |
| trnT-GGU-trnE-UUC_p4 | trnT-GGU-trnE-UUC | TGGTAAGGCATAAGTCATCGG |
GCTGCCTCCTTGAAAGAGAG |
605–618 | 1.000 | 72.8 |
| trnT-GGU-trnE-UUC_p5 | trnT-GGU-trnE-UUC | GGTAAGGCATAAGTCATCGGT |
GCTGCCTCCTTGAAAGAGAG |
604–617 | 1.000 | 72.8 |
| trnY-GUA-trnD-GUC_p1 | trnY-GUA-trnD-GUC | CTGGTTCAAATCCAGCTCGG |
CGGTGCTCTGACCAATTGAA |
389–421 | 1.000 | 80.9 |
| trnY-GUA-trnD-GUC_p2 | trnY-GUA-trnD-GUC | TCTACGCTGGTTCAAATCCA |
CGGTGCTCTGACCAATTGAA |
395–427 | 1.000 | 78.9 |
| trnY-GUA-trnD-GUC_p3 | trnY-GUA-trnD-GUC | TGGTTCAAATCCAGCTCGG |
CGGTGCTCTGACCAATTGAA |
388–420 | 1.000 | 78.2 |
| trnY-GUA-trnD-GUC_p4 | trnY-GUA-trnD-GUC | GTCTACGCTGGTTCAAATCCA |
CGGTGCTCTGACCAATTGAA |
396–428 | 1.000 | 77.6 |
| trnY-GUA-trnD-GUC_p5 | trnY-GUA-trnD-GUC | TGTCTACGCTGGTTCAAATCC |
CGGTGCTCTGACCAATTGAA |
397–429 | 1.000 | 77.6 |
| trnD-GUC-psbM_p1 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
TCATTTTGGCTGGCTGTTTT |
544–1070 | 0.909 | 65.4 |
| trnD-GUC-psbM_p2 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
AATCATTTTGGCTGGCTGTT |
546–1072 | 0.909 | 63.5 |
| trnD-GUC-psbM_p3 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
ATCATTTTGGCTGGCTGTTT |
545–1071 | 0.909 | 63.5 |
| trnD-GUC-psbM_p4 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
TCATTTTGGCTGGCTGTTTTT |
544–1070 | 0.909 | 63.3 |
| trnD-GUC-psbM_p5 | trnD-GUC-psbM | TTCAATTGGTCAGAGCACCG |
TTTGGCTGGCTGTTTTTACA |
540–1066 | 0.909 | 62.6 |
Result downloads
Reference species (22)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Oryza alta | NC_034760.1 | 135175 | View on NCBI ↗ |
| Oryza eichingeri | NC_034759.1 | 134821 | View on NCBI ↗ |
| Oryza grandiglumis | NC_034761.1 | 135150 | View on NCBI ↗ |
| Oryza latifolia | NC_034762.1 | 135190 | View on NCBI ↗ |
| Oryza longiglumis | NC_034763.1 | 135641 | View on NCBI ↗ |
| Oryza malampuzhaensis | NC_053278.1 | 134643 | View on NCBI ↗ |
| Oryza meridionalis | NC_016927.1 | 134558 | View on NCBI ↗ |
| Oryza meyeriana | NC_034765.1 | 136133 | View on NCBI ↗ |
| Oryza meyeriana var. granulata | KF359920.1 | 135942 | View on NCBI ↗ |
| Oryza minuta | NC_030298.1 | 135094 | View on NCBI ↗ |
| Oryza neocaledonica | NC_053276.1 | 135950 | View on NCBI ↗ |
| Oryza punctata | NC_027676.1 | 134604 | View on NCBI ↗ |
| Oryza rhizomatis | NC_034758.1 | 134796 | View on NCBI ↗ |
| Oryza ridleyi | NC_034764.1 | 135731 | View on NCBI ↗ |
| Oryza rufipogon | NC_017835.1 | 134544 | View on NCBI ↗ |
| Oryza sativa Indica Group | NC_008155.1 | 134496 | View on NCBI ↗ |
| Oryza sativa Japonica Group | NC_001320.1 | 134525 | View on NCBI ↗ |
| Oryza sativa | NC_031333.1 | 134502 | View on NCBI ↗ |
| Oryza sativa aromatic subgroup | KT289403.1 | 134499 | View on NCBI ↗ |
| Oryza sativa f. spontanea | NC_005973.1 | 134494 | View on NCBI ↗ |
| Oryza sativa temperate japonica subgroup | MW001303.1 | 134556 | View on NCBI ↗ |
| Oryza sativa tropical japonica subgroup | KT289404.1 | 134536 | View on NCBI ↗ |