| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rpoB-trnC-GCA | LSC | 1467 | 0.0371 | 0.95 | 79.3 | yes | View details |
| ndhF-rpl32 | SSC | 950 | 0.1829 | 0.58 | 71.4 | yes | View details |
| ycf1 | SSC | 531 | 0.0614 | 1.00 | 72.4 | yes | View details |
| trnK-UUU-rps16 | LSC | 552 | 0.0464 | 0.93 | 78.6 | yes | View details |
| rpl14-rpl16 | LSC | 140 | 0.0992 | 0.96 | 76.2 | yes | View details |
| rps16-trnQ-UUG | LSC | 948 | 0.0310 | 0.99 | 73.1 | yes | View details |
| psbM-petN | LSC | 803 | 0.0240 | 0.96 | 72.5 | yes | View details |
| atpB-rbcL | LSC | 941 | 0.0375 | 0.97 | 71.9 | yes | View details |
| trnS-GCU-trnR-UCU | LSC | 1544 | 0.0250 | 0.98 | 71.8 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 596 | 0.0263 | 0.99 | 71.7 | yes | View details |
| ndhC-trnV-UAC | LSC | 650 | 0.0331 | 0.93 | 71.3 | yes | View details |
| atpH-atpI | LSC | 584 | 0.0165 | 1.00 | 71.2 | yes | View details |
| ccsA-ndhD | SSC | 294 | 0.0519 | 0.99 | 70.8 | 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
44
Genome length
150–168 kb
Candidate markers
273
Primer pairs
65
Genome-wide nucleotide diversity
Candidate markers
3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).
Primer pairs
Showing the top 30 of 65 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
AGAAAGGAAAAACAAGAATCATGA |
521–799 | 0.932 | 49.3 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
AGAAAGGAAAAACAAGAATCATGA |
520–798 | 0.932 | 49.3 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | TACCGTTGAGTTAGCAACCC |
AGAAAGGAAAAACAAGAATCATGA |
507–785 | 0.932 | 49.3 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
AAGAAAGGAAAAACAAGAATCATGA |
522–800 | 0.932 | 49.3 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
AAGAAAGGAAAAACAAGAATCATGA |
521–799 | 0.932 | 49.3 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
ACCAACTAAAAATGGGGCGT |
929–1158 | 1.000 | 90.9 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
ACCAACTAAAAATGGGGCGT |
940–1169 | 1.000 | 90.3 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
869–1098 | 1.000 | 90.3 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
880–1109 | 1.000 | 89.8 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
CAACTAAAAATGGGGCGTGG |
927–1156 | 1.000 | 88.0 |
| trnS-GCU-trnR-UCU_p1 | trnS-GCU-trnR-UCU | CAATCCGACGCTTTAGTCCA |
AGAAGACCTCTGTCCTATCCA |
1530–1739 | 1.000 | 75.6 |
| trnS-GCU-trnR-UCU_p2 | trnS-GCU-trnR-UCU | AATCCGACGCTTTAGTCCAC |
AGAAGACCTCTGTCCTATCCA |
1529–1738 | 1.000 | 75.5 |
| trnS-GCU-trnR-UCU_p3 | trnS-GCU-trnR-UCU | CAATCCGACGCTTTAGTCCA |
AGGTTTAGAAGACCTCTGTCCT |
1536–1745 | 1.000 | 74.9 |
| trnS-GCU-trnR-UCU_p4 | trnS-GCU-trnR-UCU | AATCCGACGCTTTAGTCCAC |
AGGTTTAGAAGACCTCTGTCCT |
1535–1744 | 1.000 | 74.9 |
| trnS-GCU-trnR-UCU_p5 | trnS-GCU-trnR-UCU | AGCAATCCGACGCTTTAGTC |
AGAAGACCTCTGTCCTATCCA |
1532–1741 | 1.000 | 72.7 |
| atpH-atpI_p1 | atpH-atpI | CGCAATACCTTCTACGGCTT |
AACTTTGGCTGCGGCTTATA |
706–830 | 1.000 | 89.7 |
| atpH-atpI_p2 | atpH-atpI | TCCGATAGAAGCAAGCCCTA |
AACTTTGGCTGCGGCTTATA |
655–779 | 1.000 | 89.7 |
| atpH-atpI_p3 | atpH-atpI | AGCCAATCCAGCAGCAATAA |
AACTTTGGCTGCGGCTTATA |
634–758 | 1.000 | 89.3 |
| atpH-atpI_p4 | atpH-atpI | CCGATAGAAGCAAGCCCTAC |
AACTTTGGCTGCGGCTTATA |
654–778 | 1.000 | 89.0 |
| atpH-atpI_p5 | atpH-atpI | GCCAATCCAGCAGCAATAAC |
AACTTTGGCTGCGGCTTATA |
633–757 | 1.000 | 88.8 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | GTGGACATTCCCTCATTTCCA |
TAAAGGATTTGCAGTCCCCC |
1311–1562 | 0.932 | 76.4 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | TGTGGACATTCCCTCATTTCC |
TAAAGGATTTGCAGTCCCCC |
1312–1563 | 0.932 | 76.4 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | GTGGACATTCCCTCATTTCCA |
CGACACCCAGATTCGAACTG |
1335–1586 | 0.955 | 76.3 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | TGTGGACATTCCCTCATTTCC |
CGACACCCAGATTCGAACTG |
1336–1587 | 0.955 | 76.3 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | CCAGGTATTGTGGACATTCCC |
TAAAGGATTTGCAGTCCCCC |
1151–1571 | 0.977 | 76.1 |
| psbM-petN_p1 | psbM-petN | CTTGCGCTTATTGCTACTGC |
TAGTAAGTCTCGCTTGGGCT |
612–1012 | 1.000 | 90.0 |
| psbM-petN_p2 | psbM-petN | CTTGCGCTTATTGCTACTGC |
AGGGGACATCATTTGCATGG |
635–1035 | 1.000 | 89.5 |
| psbM-petN_p3 | psbM-petN | CTTGCGCTTATTGCTACTGC |
GGGGACATCATTTGCATGGA |
634–1034 | 1.000 | 89.5 |
| psbM-petN_p4 | psbM-petN | ACGTCAAAACAGTCAGCCAA |
TAGTAAGTCTCGCTTGGGCT |
551–951 | 1.000 | 88.8 |
| psbM-petN_p5 | psbM-petN | ATTGCTACTGCGCTGTTCAT |
TAGTAAGTCTCGCTTGGGCT |
603–1003 | 1.000 | 88.7 |
Result downloads
Reference species (44)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Cymbidium aestivum | NC_060571.1 | 149784 | View on NCBI ↗ |
| Cymbidium aloifolium | NC_021429.1 | 156904 | View on NCBI ↗ |
| Cymbidium atropurpureum | NC_060518.1 | 155379 | View on NCBI ↗ |
| Cymbidium banaense | NC_060581.1 | 155523 | View on NCBI ↗ |
| Cymbidium bicolor | MN654912.1 | 156528 | View on NCBI ↗ |
| Cymbidium bicolor subsp. pubescens | NC_060583.1 | 156578 | View on NCBI ↗ |
| Cymbidium changningense | MK848044.1 | 155388 | View on NCBI ↗ |
| Cymbidium cochleare | NC_060576.1 | 155716 | View on NCBI ↗ |
| Cymbidium cyperifolium | NC_060516.1 | 152665 | View on NCBI ↗ |
| Cymbidium daweishanense | NC_060574.1 | 156340 | View on NCBI ↗ |
| Cymbidium dayanum | NC_057616.1 | 155408 | View on NCBI ↗ |
| Cymbidium eburneum | MK820374.1 | 156520 | View on NCBI ↗ |
| Cymbidium eburneum var. longzhouense | NC_060575.1 | 155811 | View on NCBI ↗ |
| Cymbidium elegans | NC_067753.1 | 156187 | View on NCBI ↗ |
| Cymbidium ensifolium | NC_028525.1 | 157484 | View on NCBI ↗ |
| Cymbidium erythraeum | NC_053553.1 | 156327 | View on NCBI ↗ |
| Cymbidium erythraeum var. flavum | OQ405317.1 | 156062 | View on NCBI ↗ |
| Cymbidium faberi | NC_027743.1 | 157262 | View on NCBI ↗ |
| Cymbidium finlaysonianum | NC_079579.1 | 153994 | View on NCBI ↗ |
| Cymbidium floribundum | NC_063952.1 | 155382 | View on NCBI ↗ |
| Cymbidium floribundum var. pumilum | MN173778.1 | 155291 | View on NCBI ↗ |
| Cymbidium gaoligongense | NC_060578.1 | 156616 | View on NCBI ↗ |
| Cymbidium goeringii | NC_028524.1 | 157192 | View on NCBI ↗ |
| Cymbidium hartinahianum | PQ397568.1 | 150370 | View on NCBI ↗ |
| Cymbidium hookerianum | NC_053268.1 | 155447 | View on NCBI ↗ |
| Cymbidium iridioides | NC_067754.1 | 156602 | View on NCBI ↗ |
| Cymbidium kanran | NC_029711.1 | 150217 | View on NCBI ↗ |
| Cymbidium lancifolium | NC_029712.1 | 149945 | View on NCBI ↗ |
| Cymbidium longibracteatum | NC_057987.1 | 150198 | View on NCBI ↗ |
| Cymbidium lowianum | NC_050990.1 | 155447 | View on NCBI ↗ |
| Cymbidium macrorhizon | NC_029713.1 | 149850 | View on NCBI ↗ |
| Cymbidium maguanense | NC_060573.1 | 155812 | View on NCBI ↗ |
| Cymbidium mannii | NC_021433.1 | 155308 | View on NCBI ↗ |
| Cymbidium mastersii | NC_050830.1 | 156317 | View on NCBI ↗ |
| Cymbidium serratum | MT273089.1 | 149998 | View on NCBI ↗ |
| Cymbidium sichuanicum | PX549371.1 | 167769 | View on NCBI ↗ |
| Cymbidium sinense | NC_021430.1 | 155548 | View on NCBI ↗ |
| Cymbidium sinense x Cymbidium goeringii | NC_045406.1 | 150149 | View on NCBI ↗ |
| Cymbidium tortisepalum | NC_021431.1 | 155627 | View on NCBI ↗ |
| Cymbidium tracyanum | NC_021432.1 | 156286 | View on NCBI ↗ |
| Cymbidium tracyanum x Cymbidium faberi | NC_050865.1 | 154741 | View on NCBI ↗ |
| Cymbidium wenshanense | NC_060519.1 | 157740 | View on NCBI ↗ |
| Cymbidium wenshanense var. quinquelobum | NC_060577.1 | 158685 | View on NCBI ↗ |
| Cymbidium wilsonii | NC_060517.1 | 156276 | View on NCBI ↗ |