| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 278 | 0.0752 | 1.00 | 86.5 | yes | View details |
| trnK-UUU-rps16 | LSC | 673 | 0.0381 | 0.99 | 81.4 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 818 | 0.0293 | 0.98 | 81.6 | yes | View details |
| trnL-UAA-trnF-GAA | LSC | 532 | 0.0420 | 0.86 | 74.2 | yes | View details |
| ndhC-trnV-UAC | LSC | 917 | 0.0337 | 0.95 | 79.6 | yes | View details |
| psbE-petL | LSC | 1349 | 0.0279 | 0.99 | 77.8 | yes | View details |
| psaJ-rpl33 | LSC | 434 | 0.0388 | 0.98 | 79.4 | yes | View details |
| ycf1 | IRb | 1032 | 0.0052 | 1.00 | 47.3 | no | View details |
| ndhF-rpl32 | SSC | 841 | 0.0357 | 0.98 | 81.4 | yes | View details |
| rpl32-trnL-UAG | SSC | 779 | 0.0462 | 0.99 | 84.4 | yes | View details |
| ycf1 | SSC | 5394 | 0.0225 | 1.00 | 68.6 | yes | View details |
| psaA-ycf3 | LSC | 724 | 0.0167 | 1.00 | 84.7 | yes | View details |
| psbK-psbI | LSC | 418 | 0.0352 | 1.00 | 82.1 | yes | View details |
| rbcL-accD | LSC | 681 | 0.0210 | 1.00 | 81.4 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 687 | 0.0264 | 0.96 | 79.0 | yes | View details |
| trnF-GAA-ndhJ | LSC | 602 | 0.0245 | 0.98 | 78.2 | yes | View details |
| trnT-GGU-psbD | LSC | 1237 | 0.0239 | 0.99 | 77.6 | yes | View details |
| rps4-trnT-UGU | LSC | 386 | 0.0194 | 1.00 | 76.8 | yes | View details |
| trnG-UCC-trnR-UCU | LSC | 159 | 0.0417 | 1.00 | 76.3 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 677 | 0.0314 | 0.99 | 75.7 | 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
25
Genome length
154–156 kb
Candidate markers
267
Primer pairs
95
Genome-wide nucleotide diversity
Candidate markers
11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 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 |
|---|---|---|---|---|---|---|
| trnH-GUG-psbA_p1 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
GCTGTTGAGGCTCCATCTAC |
235–376 | 1.000 | 90.5 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
TTCCCTCTAGACCTAGCTGC |
253–394 | 1.000 | 90.3 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | ACTGCCTTAATCCACTTGGC |
GCTGTTGAGGCTCCATCTAC |
236–377 | 1.000 | 90.3 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
CCTCTAGACCTAGCTGCTGT |
250–391 | 0.960 | 88.8 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | ACTGCCTTAATCCACTTGGC |
CCTCTAGACCTAGCTGCTGT |
251–392 | 0.960 | 88.6 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | CCTTTCAGGATCAGTCGTGG |
CCCAATGAGCCGTTTATCGA |
150–1096 | 1.000 | 91.5 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | CCTTTCAGGATCAGTCGTGG |
TCCCAATGAGCCGTTTATCG |
149–1097 | 1.000 | 91.5 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | TCAGGATCAGTCGTGGTCTT |
CCCAATGAGCCGTTTATCGA |
146–1092 | 1.000 | 91.0 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | TCAGGATCAGTCGTGGTCTT |
TCCCAATGAGCCGTTTATCG |
145–1093 | 1.000 | 91.0 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | TTCAGGATCAGTCGTGGTCT |
CCCAATGAGCCGTTTATCGA |
147–1093 | 1.000 | 91.0 |
| psbK-psbI_p1 | psbK-psbI | CAAGCCGCTGTAAGTTTTCG |
TTCTTCACGTCCCGGATTAC |
417–561 | 1.000 | 86.3 |
| psbK-psbI_p2 | psbK-psbI | AGCCGCTGTAAGTTTTCGAT |
TTCTTCACGTCCCGGATTAC |
415–559 | 1.000 | 86.0 |
| psbK-psbI_p3 | psbK-psbI | AAGCCGCTGTAAGTTTTCGA |
TTCTTCACGTCCCGGATTAC |
416–560 | 1.000 | 85.7 |
| psbK-psbI_p4 | psbK-psbI | GCCGCTGTAAGTTTTCGATG |
TTCTTCACGTCCCGGATTAC |
414–558 | 1.000 | 85.4 |
| psbK-psbI_p5 | psbK-psbI | GCAAGCCGCTGTAAGTTTTC |
TTCTTCACGTCCCGGATTAC |
418–562 | 1.000 | 84.2 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | CAAGCCGCTGTAAGTTTTCG |
AAGGGTTTTAGTCGACGTCG |
2032–2183 | 1.000 | 91.2 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | AGCCGCTGTAAGTTTTCGAT |
AAGGGTTTTAGTCGACGTCG |
2030–2181 | 1.000 | 90.8 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | AAGCCGCTGTAAGTTTTCGA |
AAGGGTTTTAGTCGACGTCG |
2031–2182 | 1.000 | 90.5 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | CAAGCCGCTGTAAGTTTTCG |
CGTATGGGTGCTTTCACAGA |
1853–2000 | 0.800 | 82.9 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AGCCGCTGTAAGTTTTCGAT |
CGTATGGGTGCTTTCACAGA |
1851–1998 | 0.800 | 82.5 |
| trnG-UCC-trnR-UCU_p1 | trnG-UCC-trnR-UCU | ACCCTTAGCCTTCCAAGCTA |
TGATATTGCGTCCAATAGGA |
277–289 | 1.000 | 58.8 |
| trnG-UCC-trnR-UCU_p2 | trnG-UCC-trnR-UCU | CGACGTCGACTAAAACCCTT |
TGATATTGCGTCCAATAGGA |
291–303 | 1.000 | 58.4 |
| trnG-UCC-trnR-UCU_p3 | trnG-UCC-trnR-UCU | AAACCCTTAGCCTTCCAAGC |
TGATATTGCGTCCAATAGGA |
279–291 | 1.000 | 58.4 |
| trnG-UCC-trnR-UCU_p4 | trnG-UCC-trnR-UCU | AGCCTTCCAAGCTAACGATG |
TGATATTGCGTCCAATAGGA |
271–283 | 0.960 | 57.3 |
| trnG-UCC-trnR-UCU_p5 | trnG-UCC-trnR-UCU | AGCCTTCCAAGCTAACGATG |
TTGATATTGCGTCCAATAGGA |
272–284 | 0.960 | 56.3 |
| trnE-UUC-trnT-GGU_p1 | trnE-UUC-trnT-GGU | TTTCGTAGTACCCTACCCCC |
GAACCGATGACTTACGCCTT |
586–980 | 1.000 | 90.7 |
| trnE-UUC-trnT-GGU_p2 | trnE-UUC-trnT-GGU | TTTCGTAGTACCCTACCCCC |
CCATGGCGTTACTCTACCAC |
565–959 | 1.000 | 90.2 |
| trnE-UUC-trnT-GGU_p3 | trnE-UUC-trnT-GGU | TTTCGTAGTACCCTACCCCC |
TGGCGTTACTCTACCACTGA |
562–956 | 1.000 | 90.0 |
| trnE-UUC-trnT-GGU_p4 | trnE-UUC-trnT-GGU | GCTGCCTCCTTGAAAGAGAG |
GAACCGATGACTTACGCCTT |
548–942 | 1.000 | 89.8 |
| trnE-UUC-trnT-GGU_p5 | trnE-UUC-trnT-GGU | TGTCCTGAACCACTAGACGA |
GAACCGATGACTTACGCCTT |
527–921 | 1.000 | 89.7 |
Result downloads
Reference species (25)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Cardamine abchasica | NC_060863.1 | 155383 | View on NCBI ↗ |
| Cardamine amara | NC_036962.1 | 154561 | View on NCBI ↗ |
| Cardamine amariformis | MZ043776.1 | 155598 | View on NCBI ↗ |
| Cardamine anhuiensis | PP719683.1 | 154276 | View on NCBI ↗ |
| Cardamine bipinnata | NC_060865.1 | 155264 | View on NCBI ↗ |
| Cardamine bulbifera | NC_049603.1 | 155295 | View on NCBI ↗ |
| Cardamine engleriana | PP719684.1 | 155325 | View on NCBI ↗ |
| Cardamine enneaphyllos | NC_049605.1 | 155221 | View on NCBI ↗ |
| Cardamine fallax | MZ043778.1 | 154797 | View on NCBI ↗ |
| Cardamine fragariifolia | PP719685.1 | 154829 | View on NCBI ↗ |
| Cardamine glanduligera | NC_049606.1 | 153828 | View on NCBI ↗ |
| Cardamine heptaphylla | NC_060864.1 | 155112 | View on NCBI ↗ |
| Cardamine hirsuta | NC_049607.1 | 153934 | View on NCBI ↗ |
| Cardamine hupingshanensis | NC_065146.1 | 155226 | View on NCBI ↗ |
| Cardamine hygrophila | PP719686.1 | 155307 | View on NCBI ↗ |
| Cardamine impatiens | NC_026445.1 | 155611 | View on NCBI ↗ |
| Cardamine kitaibelii | NC_049610.1 | 155160 | View on NCBI ↗ |
| Cardamine lyrata | NC_062128.1 | 155170 | View on NCBI ↗ |
| Cardamine macrophylla | MF405340.1 | 155393 | View on NCBI ↗ |
| Cardamine oligosperma | NC_036963.1 | 153888 | View on NCBI ↗ |
| Cardamine parviflora | NC_036964.1 | 154684 | View on NCBI ↗ |
| Cardamine pentaphyllos | NC_049617.1 | 155560 | View on NCBI ↗ |
| Cardamine quinquefolia | NC_049620.1 | 155009 | View on NCBI ↗ |
| Cardamine resedifolia | NC_026446.1 | 155036 | View on NCBI ↗ |
| Cardamine zhangjiajieensis | PP114745.1 | 155413 | View on NCBI ↗ |