| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16-trnQ-UUG | LSC | 1114 | 0.0467 | 0.94 | 85.7 | yes | View details |
| trnS-GCU-trnG-GCC | LSC | 1154 | 0.0351 | 0.93 | 74.9 | yes | View details |
| rpoB-trnC-GCA | LSC | 1427 | 0.0196 | 0.98 | 71.8 | yes | View details |
| trnC-GCA-petN | LSC | 639 | 0.0153 | 0.99 | 64.4 | yes | View details |
| petN-psbM | LSC | 843 | 0.0281 | 0.97 | 67.1 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 829 | 0.0278 | 0.94 | 68.4 | yes | View details |
| atpB-rbcL | LSC | 974 | 0.0285 | 0.98 | 70.1 | yes | View details |
| psbB-psbT | LSC | 607 | 0.0344 | 0.97 | 72.4 | yes | View details |
| ndhF-rpl32 | SSC | 1019 | 0.0251 | 0.95 | 69.2 | yes | View details |
| ycf4-cemA | LSC | 768 | 0.0193 | 0.99 | 70.7 | yes | View details |
| trnV-GAC-rps12 | IRa | 1239 | 0.0137 | 0.95 | 68.8 | yes | View details |
| ndhC-trnV-UAC | LSC | 1409 | 0.0208 | 0.99 | 68.3 | yes | View details |
| rps12-trnV-GAC | IRb | 1239 | 0.0130 | 0.95 | 68.2 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 586 | 0.0224 | 0.99 | 66.7 | yes | View details |
| matK-trnK-UUU | LSC | 1049 | 0.0231 | 0.92 | 66.6 | yes | View details |
| clpP-psbB | LSC | 800 | 0.0221 | 0.95 | 66.6 | yes | View details |
| psaJ-rpl33 | LSC | 558 | 0.0210 | 1.00 | 64.7 | yes | View details |
| trnR-ACG-trnN-GUU | IRb | 518 | 0.0075 | 1.00 | 64.6 | 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
38
Genome length
157–159 kb
Candidate markers
279
Primer pairs
95
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 279 candidates).
Primer pairs
Showing the top 30 of 95 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| trnK-UUU_p1 | trnK-UUU | TCGCGACGAGAATGGAATTT |
CCTGATGTGGGGAAAGGTTC |
906–1159 | 0.974 | 89.6 |
| trnK-UUU_p2 | trnK-UUU | GTCAGAACGGCGTATGCATA |
GATTAGTGCCTGATGTGGGG |
642–691 | 0.237 | 54.1 |
| trnK-UUU_p3 | trnK-UUU | TCGCGACGAGAATGGAATTT |
GATTAGTGCCTGATGTGGGG |
1074–1123 | 0.237 | 53.1 |
| trnK-UUU_p4 | trnK-UUU | GCCCCCAAAAACCATTTTCC |
GATTAGTGCCTGATGTGGGG |
988–1037 | 0.237 | 52.7 |
| trnK-UUU_p5 | trnK-UUU | ACTAATCGCGACGAGAATGG |
GATTAGTGCCTGATGTGGGG |
1079–1128 | 0.237 | 52.1 |
| matK-trnK-UUU_p1 | matK-trnK-UUU | AGGAAGTTTTGTTGCCGAAA |
ATCCGGGTTGCTAACTCAAC |
993–1288 | 1.000 | 78.1 |
| matK-trnK-UUU_p2 | matK-trnK-UUU | AGGAAGTTTTGTTGCCGAAA |
AACGGTAGAGTACTCGGCTT |
976–1271 | 1.000 | 77.6 |
| matK-trnK-UUU_p3 | matK-trnK-UUU | AGGAAGTTTTGTTGCCGAAA |
ACGGTAGAGTACTCGGCTTT |
975–1270 | 1.000 | 77.6 |
| matK-trnK-UUU_p4 | matK-trnK-UUU | AGGAAGTTTTGTTGCCGAAA |
GATCCGGGTTGCTAACTCAA |
994–1289 | 1.000 | 75.8 |
| matK-trnK-UUU_p5 | matK-trnK-UUU | AGGAAGTTTTGTTGCCGAAA |
TTGATCCGGGTTGCTAACTC |
996–1291 | 1.000 | 75.8 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | ATCCACAGCCAATCATGTCC |
GACCAAATCAAAATGGGGCG |
1083–1444 | 1.000 | 91.4 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | ATCCACAGCCAATCATGTCC |
GAGGTTCGAATCCTTCCGTC |
1022–1383 | 1.000 | 90.9 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GACCAAATCAAAATGGGGCG |
1060–1421 | 1.000 | 90.8 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CCACAGCCAATCATGTCCTT |
GACCAAATCAAAATGGGGCG |
1081–1442 | 1.000 | 90.7 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GACCAAATCAAAATGGGGCG |
1071–1432 | 1.000 | 90.3 |
| trnS-GCU-trnG-GCC_p1 | trnS-GCU-trnG-GCC | CAATCCGACGCTTTAGTCCA |
ACGAATCACACTTTTACCACT |
992–1246 | 1.000 | 63.7 |
| trnS-GCU-trnG-GCC_p2 | trnS-GCU-trnG-GCC | AATCCGACGCTTTAGTCCAC |
ACGAATCACACTTTTACCACT |
991–1245 | 1.000 | 63.7 |
| trnS-GCU-trnG-GCC_p3 | trnS-GCU-trnG-GCC | CAATCCGACGCTTTAGTCCA |
AGAACGAATCACACTTTTACCAC |
995–1249 | 1.000 | 62.6 |
| trnS-GCU-trnG-GCC_p4 | trnS-GCU-trnG-GCC | CAATCCGACGCTTTAGTCCA |
GAACGAATCACACTTTTACCACT |
994–1248 | 1.000 | 62.6 |
| trnS-GCU-trnG-GCC_p5 | trnS-GCU-trnG-GCC | AATCCGACGCTTTAGTCCAC |
GAACGAATCACACTTTTACCACT |
993–1247 | 1.000 | 62.6 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | AATTCTTCCGTCAAGCCCTG |
TAAAGGATTTGCAGTCCCCC |
1187–1643 | 1.000 | 86.4 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | AATTCTTCCGTCAAGCCCTG |
CGACACCCAGATTCGAACTG |
1211–1667 | 1.000 | 85.4 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | AATTCTTCCGTCAAGCCCTG |
TTTGTTGATCAGGCGACACC |
1224–1680 | 1.000 | 84.5 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | AAATTCTTCCGTCAAGCCCT |
TAAAGGATTTGCAGTCCCCC |
1188–1644 | 1.000 | 83.1 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | AATTCTTCCGTCAAGCCCTG |
ATAAAGGATTTGCAGTCCCCC |
1188–1644 | 1.000 | 82.4 |
| trnC-GCA-petN_p1 | trnC-GCA-petN | CCAGTTCGAATCTGGGTGTC |
GCTCTAAAGCCCACTCCTTC |
487–940 | 1.000 | 86.8 |
| trnC-GCA-petN_p2 | trnC-GCA-petN | CCAGTTCGAATCTGGGTGTC |
AGCCCAAGCGAGACTTACTA |
421–874 | 1.000 | 86.1 |
| trnC-GCA-petN_p3 | trnC-GCA-petN | GGGGGACTGCAAATCCTTTA |
GCTCTAAAGCCCACTCCTTC |
510–963 | 1.000 | 84.6 |
| trnC-GCA-petN_p4 | trnC-GCA-petN | GGGGGACTGCAAATCCTTTA |
AGCCCAAGCGAGACTTACTA |
444–897 | 1.000 | 84.0 |
| trnC-GCA-petN_p5 | trnC-GCA-petN | CAGTTCGAATCTGGGTGTCG |
GCTCTAAAGCCCACTCCTTC |
486–939 | 1.000 | 83.8 |
Result downloads
Reference species (38)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Calanthe alismifolia | NC_084137.1 | 158078 | View on NCBI ↗ |
| Calanthe alleizettei | NC_084138.1 | 158251 | View on NCBI ↗ |
| Calanthe angustifolia | NC_084139.1 | 157126 | View on NCBI ↗ |
| Calanthe arcuata | NC_058650.1 | 158735 | View on NCBI ↗ |
| Calanthe arcuata var. brevifolia | OK180390.1 | 158695 | View on NCBI ↗ |
| Calanthe argenteostriata | NC_084140.1 | 158139 | View on NCBI ↗ |
| Calanthe arisanensis | NC_084141.1 | 158876 | View on NCBI ↗ |
| Calanthe aristulifera | NC_046812.1 | 158204 | View on NCBI ↗ |
| Calanthe bicolor | NC_046813.1 | 158070 | View on NCBI ↗ |
| Calanthe brevicornu | NC_067586.1 | 158384 | View on NCBI ↗ |
| Calanthe cardioglossa | NC_084142.1 | 159299 | View on NCBI ↗ |
| Calanthe clavata | NC_071937.1 | 157641 | View on NCBI ↗ |
| Calanthe columnaris | NC_084157.1 | 157982 | View on NCBI ↗ |
| Calanthe densiflora | NC_084143.1 | 157609 | View on NCBI ↗ |
| Calanthe discolor | NC_068094.1 | 158286 | View on NCBI ↗ |
| Calanthe flava | NC_067591.1 | 158556 | View on NCBI ↗ |
| Calanthe graciliflora | NC_072910.1 | 158214 | View on NCBI ↗ |
| Calanthe griffithii | NC_084144.1 | 158274 | View on NCBI ↗ |
| Calanthe hancockii | NC_064068.1 | 158285 | View on NCBI ↗ |
| Calanthe henryi | NC_054177.1 | 158256 | View on NCBI ↗ |
| Calanthe herbacea | NC_062706.1 | 158741 | View on NCBI ↗ |
| Calanthe lamellosa | NC_084145.1 | 158454 | View on NCBI ↗ |
| Calanthe lechangensis | NC_084146.1 | 158222 | View on NCBI ↗ |
| Calanthe mannii | NC_084147.1 | 158062 | View on NCBI ↗ |
| Calanthe mcgregorii | NC_084148.1 | 158891 | View on NCBI ↗ |
| Calanthe metoensis | NC_084149.1 | 158208 | View on NCBI ↗ |
| Calanthe nipponica | NC_067588.1 | 158714 | View on NCBI ↗ |
| Calanthe reflexa | NC_062707.1 | 158842 | View on NCBI ↗ |
| Calanthe rubens | NC_050869.1 | 158215 | View on NCBI ↗ |
| Calanthe sinica | NC_084150.1 | 158843 | View on NCBI ↗ |
| Calanthe striata var. sieboldii | OK180408.1 | 158299 | View on NCBI ↗ |
| Calanthe sylvatica | NC_044633.1 | 158828 | View on NCBI ↗ |
| Calanthe taibaishanensis | NC_067589.1 | 157959 | View on NCBI ↗ |
| Calanthe trifida | NC_084151.1 | 158330 | View on NCBI ↗ |
| Calanthe triplicata | NC_024544.1 | 158759 | View on NCBI ↗ |
| Calanthe tsoongiana | NC_080272.1 | 158042 | View on NCBI ↗ |
| Calanthe yaoshanensis | NC_084152.1 | 158360 | View on NCBI ↗ |
| Calanthe yuana | NC_084153.1 | 158255 | View on NCBI ↗ |