| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 432 | 0.0103 | 1.00 | 57.5 | yes | View details |
| trnK-UUU-rps16 | LSC | 1471 | 0.0055 | 0.99 | 71.1 | yes | View details |
| trnS-UGA-psbZ | LSC | 356 | 0.0017 | 1.00 | 40.2 | yes | View details |
| psaA-ycf3 | LSC | 763 | 0.0078 | 1.00 | 70.9 | yes | View details |
| accD-psaI | LSC | 847 | 0.0076 | 1.00 | 66.2 | yes | View details |
| rps12-clpP | LSC | 1186 | 0.0067 | 1.00 | 73.3 | yes | View details |
| ycf1 | IRb | 2269 | 0.0017 | 0.99 | 35.5 | yes | View details |
| ndhF-rpl32 | SSC | 679 | 0.0097 | 0.98 | 66.9 | yes | View details |
| rpl32-trnL-UAG | SSC | 761 | 0.0125 | 1.00 | 67.9 | yes | View details |
| ndhD | SSC | 1503 | 0.0018 | 1.00 | 40.9 | yes | View details |
| ycf1 | SSC | 5733 | 0.0026 | 1.00 | 58.4 | no | View details |
| psbI-trnS-GCU | LSC | 165 | 0.0225 | 0.99 | 77.2 | yes | View details |
| infA-rps8 | LSC | 81 | 0.0268 | 1.00 | 66.2 | yes | View details |
| petA-psbJ | LSC | 622 | 0.0074 | 1.00 | 64.3 | yes | View details |
| ndhC-trnV-UAC | LSC | 1678 | 0.0039 | 1.00 | 62.5 | yes | View details |
| psbE-petL | LSC | 654 | 0.0034 | 0.99 | 62.0 | yes | View details |
| rpl22-trnH-GUG | LSC | 76 | 0.0874 | 0.89 | 61.0 | no | View details |
| petN-psbM | LSC | 1117 | 0.0019 | 0.98 | 60.1 | yes | View details |
| psbT-psbN | LSC | 75 | 0.0376 | 1.00 | 60.1 | yes | View details |
| ndhD-psaC | SSC | 135 | 0.0393 | 0.99 | 59.8 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 853 | 0.0051 | 1.00 | 59.3 | 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
48
Genome length
157–165 kb
Candidate markers
275
Primer pairs
95
Genome-wide nucleotide diversity
Candidate markers
11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 275 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 |
465–501 | 0.979 | 89.2 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | ACTGCCTTAATCCACTTGGC |
GCTGTTGAGGCTCCATCTAC |
466–502 | 0.979 | 89.0 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
GCGCTAACCTTGGTATGGAA |
530–566 | 0.979 | 88.5 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACTGCCTTAATCCACTTGGC |
GCGCTAACCTTGGTATGGAA |
531–567 | 0.979 | 88.2 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | CTGCCTTAATCCACTTGGCT |
TATCATCAACCGCGCTAACC |
541–577 | 0.979 | 87.5 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
TGTTCTACGAACAAGGAAGCT |
1369–1534 | 0.938 | 70.4 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
TGTTCTACGAACAAGGAAGCT |
1368–1533 | 0.938 | 70.4 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | TACCGTTGAGTTAGCAACCC |
TGTTCTACGAACAAGGAAGCT |
1355–1520 | 0.938 | 68.1 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
TTGTTCTACGAACAAGGAAGCT |
1370–1535 | 0.938 | 67.8 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
TTGTTCTACGAACAAGGAAGCT |
1369–1534 | 0.938 | 67.8 |
| psbI-trnS-GCU_p1 | psbI-trnS-GCU | CTATCGAATGATCCAGGGCG |
ATTGGGAGAGATGGCTGAGT |
209–314 | 0.979 | 89.6 |
| psbI-trnS-GCU_p2 | psbI-trnS-GCU | CGAATGATCCAGGGCGTAAT |
ATTGGGAGAGATGGCTGAGT |
205–310 | 1.000 | 89.5 |
| psbI-trnS-GCU_p3 | psbI-trnS-GCU | CTATCGAATGATCCAGGGCG |
CTTCTTCGTACCGAGGGTTC |
154–259 | 0.979 | 89.0 |
| psbI-trnS-GCU_p4 | psbI-trnS-GCU | CTATCGAATGATCCAGGGCG |
GTGGACTAAAGCGGCTGATT |
191–296 | 0.979 | 88.9 |
| psbI-trnS-GCU_p5 | psbI-trnS-GCU | CTATCGAATGATCCAGGGCG |
TGGACTAAAGCGGCTGATTG |
190–295 | 0.979 | 88.9 |
| petN-psbM_p1 | petN-psbM | TCTTGCTTGGGCTGCATTAA |
TGTTCATTCTAATCCCTACGGC |
1226–1261 | 1.000 | 68.8 |
| petN-psbM_p2 | petN-psbM | AGTAAGTCTTGCTTGGGCTG |
TGTTCATTCTAATCCCTACGGC |
1232–1267 | 1.000 | 67.9 |
| petN-psbM_p3 | petN-psbM | ATGGGGAAGAAGTGGACTCT |
TGTTCATTCTAATCCCTACGGC |
1172–1207 | 1.000 | 66.7 |
| petN-psbM_p4 | petN-psbM | TCTTGCTTGGGCTGCATTAA |
GTTCATTCTAATCCCTACGGCT |
1225–1260 | 1.000 | 66.6 |
| petN-psbM_p5 | petN-psbM | TCTTGCTTGGGCTGCATTAA |
ACGTAAAAACGGTCAGTCAA |
1187–1222 | 1.000 | 65.9 |
| trnS-UGA-psbZ_p1 | trnS-UGA-psbZ | CAAGACCGGAGCTATCAACC |
CGCAAAAACAGCCAATTGGA |
413–431 | 1.000 | 84.0 |
| trnS-UGA-psbZ_p2 | trnS-UGA-psbZ | CAAGACCGGAGCTATCAACC |
GACCAACCCTCAGAAGAAGC |
481–499 | 1.000 | 83.5 |
| trnS-UGA-psbZ_p3 | trnS-UGA-psbZ | CTATCAACCACTCGGCCATC |
CGCAAAAACAGCCAATTGGA |
402–420 | 1.000 | 83.4 |
| trnS-UGA-psbZ_p4 | trnS-UGA-psbZ | CTATCAACCACTCGGCCATC |
GACCAACCCTCAGAAGAAGC |
470–488 | 1.000 | 83.0 |
| trnS-UGA-psbZ_p5 | trnS-UGA-psbZ | CAAGACCGGAGCTATCAACC |
CCAACCCTCAGAAGAAGCAA |
479–497 | 1.000 | 82.8 |
| psaA-ycf3_p1 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
GGAAACAGGCTATAGCGCTT |
904–935 | 1.000 | 86.4 |
| psaA-ycf3_p2 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
TTGGTTGAAGATCACGAGGC |
855–886 | 1.000 | 85.7 |
| psaA-ycf3_p3 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
AGCCGCTGAGTATTGGAAAC |
918–949 | 1.000 | 84.6 |
| psaA-ycf3_p4 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
CAAGCCGCTGAGTATTGGAA |
920–951 | 1.000 | 84.6 |
| psaA-ycf3_p5 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
TAGCGCTTACTCCGGGTAAT |
892–923 | 1.000 | 84.5 |
Result downloads
Reference species (48)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Epimedium acuminatum | NC_029941.1 | 159112 | View on NCBI ↗ |
| Epimedium alpinum | MW483082.1 | 157224 | View on NCBI ↗ |
| Epimedium baojingense | NC_062452.1 | 156749 | View on NCBI ↗ |
| Epimedium borealiguizhouense | NC_044889.1 | 157281 | View on NCBI ↗ |
| Epimedium brachyrrhizum | PV192904.1 | 157154 | View on NCBI ↗ |
| Epimedium brevicornu | NC_046776.1 | 156947 | View on NCBI ↗ |
| Epimedium campanulatum | MW470954.1 | 157343 | View on NCBI ↗ |
| Epimedium chlorandrum | NC_044892.1 | 158251 | View on NCBI ↗ |
| Epimedium coactum | PV192907.1 | 157070 | View on NCBI ↗ |
| Epimedium davidii | NC_053384.1 | 159715 | View on NCBI ↗ |
| Epimedium diphyllum | MW483080.1 | 157180 | View on NCBI ↗ |
| Epimedium dolichostemon | NC_029942.1 | 157039 | View on NCBI ↗ |
| Epimedium ecalcaratum | NC_053530.1 | 164962 | View on NCBI ↗ |
| Epimedium elatum | MW483094.1 | 156897 | View on NCBI ↗ |
| Epimedium elongatum | PV192915.1 | 158995 | View on NCBI ↗ |
| Epimedium enshiense | MN937557.1 | 157076 | View on NCBI ↗ |
| Epimedium epsteinii | MT560404.1 | 157180 | View on NCBI ↗ |
| Epimedium fangii | OQ366389.1 | 159153 | View on NCBI ↗ |
| Epimedium fargesii | NC_058850.1 | 157133 | View on NCBI ↗ |
| Epimedium flavum | NC_059690.1 | 159134 | View on NCBI ↗ |
| Epimedium franchetii | NC_065479.1 | 156773 | View on NCBI ↗ |
| Epimedium glandulosopilosum | PV192916.1 | 157341 | View on NCBI ↗ |
| Epimedium hunanense | MW483089.1 | 157209 | View on NCBI ↗ |
| Epimedium ilicifolium | NC_044897.1 | 156855 | View on NCBI ↗ |
| Epimedium jinchengshanense | NC_058849.1 | 157169 | View on NCBI ↗ |
| Epimedium latisepalum | MW483079.1 | 158227 | View on NCBI ↗ |
| Epimedium membranaceum | MW483091.1 | 159088 | View on NCBI ↗ |
| Epimedium mikinorii | NC_044890.1 | 156984 | View on NCBI ↗ |
| Epimedium muhuangense | NC_063320.1 | 157264 | View on NCBI ↗ |
| Epimedium myrianthum | MT560399.1 | 156635 | View on NCBI ↗ |
| Epimedium parvifolium | NC_053526.1 | 157201 | View on NCBI ↗ |
| Epimedium pauciflorum | PV192912.1 | 159159 | View on NCBI ↗ |
| Epimedium pseudowushanense | NC_029945.1 | 157168 | View on NCBI ↗ |
| Epimedium pubescens | NC_053532.1 | 158956 | View on NCBI ↗ |
| Epimedium pubigerum | MW483081.1 | 157085 | View on NCBI ↗ |
| Epimedium pudingense | NC_048880.1 | 157325 | View on NCBI ↗ |
| Epimedium qingchengshanense | NC_053539.1 | 159087 | View on NCBI ↗ |
| Epimedium rhizomatosum | NC_053531.1 | 159150 | View on NCBI ↗ |
| Epimedium shuichengense | NC_053528.1 | 157046 | View on NCBI ↗ |
| Epimedium stellulatum | NC_065478.1 | 157196 | View on NCBI ↗ |
| Epimedium stellulatum x Epimedium franchetii | NC_065480.1 | 156767 | View on NCBI ↗ |
| Epimedium sutchuenense | NC_058848.1 | 157263 | View on NCBI ↗ |
| Epimedium tianmenshanensis | NC_053540.1 | 157066 | View on NCBI ↗ |
| Epimedium trifoliolatobinatum | MW483095.1 | 157272 | View on NCBI ↗ |
| Epimedium truncatum | NC_062455.1 | 157044 | View on NCBI ↗ |
| Epimedium wushanense | NC_044891.1 | 157194 | View on NCBI ↗ |
| Epimedium xichangense | NC_046945.1 | 158955 | View on NCBI ↗ |
| Epimedium zhushanense | NC_065696.1 | 157057 | View on NCBI ↗ |