| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 410 | 0.0489 | 0.96 | 74.5 | yes | View details |
| rps16-trnQ-UUG | LSC | 1274 | 0.0177 | 0.97 | 69.2 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 978 | 0.0211 | 0.99 | 75.5 | yes | View details |
| rpoB-trnC-GCA | LSC | 1104 | 0.0167 | 0.99 | 73.5 | yes | View details |
| psbZ-trnG-GCC | LSC | 499 | 0.0340 | 1.00 | 74.8 | yes | View details |
| rps3 | LSC | 660 | 0.0079 | 1.00 | 44.5 | yes | View details |
| ycf1 | IRb | 1809 | 0.0089 | 0.68 | 48.0 | yes | View details |
| ndhF-rpl32 | SSC | 975 | 0.0233 | 0.98 | 70.4 | yes | View details |
| rpl32-trnL-UAG | SSC | 644 | 0.0212 | 0.97 | 69.1 | yes | View details |
| ycf1 | SSC | 5487 | 0.0123 | 1.00 | 51.7 | no | View details |
| trnE-UUC-trnT-GGU | LSC | 808 | 0.0149 | 1.00 | 79.3 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 987 | 0.0150 | 1.00 | 75.2 | yes | View details |
| accD-psaI | LSC | 699 | 0.0162 | 1.00 | 73.0 | yes | View details |
| ndhC-trnV-UAC | LSC | 417 | 0.0145 | 1.00 | 71.9 | yes | View details |
| psaA-ycf3 | LSC | 707 | 0.0140 | 1.00 | 70.7 | yes | View details |
| trnD-GUC-trnY-GUA | LSC | 490 | 0.0164 | 0.98 | 70.3 | yes | View details |
| trnC-GCA-petN | LSC | 719 | 0.0136 | 0.98 | 69.4 | yes | View details |
| psbA-trnK-UUU | LSC | 270 | 0.0156 | 0.99 | 69.3 | yes | View details |
| ndhE-ndhG | SSC | 251 | 0.0199 | 1.00 | 69.1 | yes | View details |
| atpH-atpI | LSC | 1276 | 0.0136 | 0.99 | 66.7 | 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
31
Genome length
157–159 kb
Candidate markers
272
Primer pairs
95
Genome-wide nucleotide diversity
Candidate markers
10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 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 | GATCCACTTGGCTACATCCG |
TCAGTGCTATGCATGGTTCC |
705–886 | 1.000 | 90.6 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
TCAGTGCTATGCATGGTTCC |
719–900 | 1.000 | 90.6 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
CAGTGCTATGCATGGTTCCT |
704–885 | 1.000 | 90.6 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
TCAGTGCTATGCATGGTTCC |
718–899 | 1.000 | 90.6 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
TCAGTGCTATGCATGGTTCC |
720–901 | 1.000 | 90.6 |
| psbA-trnK-UUU_p1 | psbA-trnK-UUU | CCGTTTTCGCGTCTCTCTAA |
ACTCCATCCGACTAGTTCCG |
335–363 | 1.000 | 85.2 |
| psbA-trnK-UUU_p2 | psbA-trnK-UUU | CCGTTTTCGCGTCTCTCTAA |
GAAAAATGCATGCACGGCTT |
396–423 | 1.000 | 85.0 |
| psbA-trnK-UUU_p3 | psbA-trnK-UUU | CCGTTTTCGCGTCTCTCTAA |
ATGAAAAATGCATGCACGGC |
398–425 | 1.000 | 84.4 |
| psbA-trnK-UUU_p4 | psbA-trnK-UUU | ATGTAAAGGCGGTTTTCGGT |
ACTCCATCCGACTAGTTCCG |
392–420 | 1.000 | 84.2 |
| psbA-trnK-UUU_p5 | psbA-trnK-UUU | ATGTAAAGGCGGTTTTCGGT |
GAAAAATGCATGCACGGCTT |
453–480 | 1.000 | 83.9 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | CAGCGGATCATGTCCTTCAA |
GAGGTTCGAATCCTTCCGTC |
355–1365 | 1.000 | 91.2 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | GCGGATCATGTCCTTCAAGT |
GAGGTTCGAATCCTTCCGTC |
353–1363 | 1.000 | 91.2 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | CAGCGGATCATGTCCTTCAA |
GAAATTGAAATGGGGCGTCG |
413–1423 | 1.000 | 91.0 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | GCGGATCATGTCCTTCAAGT |
GAAATTGAAATGGGGCGTCG |
411–1421 | 1.000 | 91.0 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
337–1347 | 1.000 | 90.3 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | CCGACGCTTTAATCCACTCA |
TGAACGAATCACACTTTTACCAC |
889–1080 | 1.000 | 64.7 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | CCGACGCTTTAATCCACTCA |
ACGAATCACACTTTTACCACT |
886–1077 | 1.000 | 63.7 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
TGAACGAATCACACTTTTACCAC |
947–1138 | 1.000 | 63.5 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | CCGACGCTTTAATCCACTCA |
GAACGAATCACACTTTTACCACT |
888–1079 | 1.000 | 62.6 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | ACGCTTTAATCCACTCAGCC |
TGAACGAATCACACTTTTACCAC |
886–1077 | 1.000 | 62.6 |
| atpH-atpI_p1 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TCTATGGAGGGACATCATTGA |
1291–1357 | 1.000 | 63.7 |
| atpH-atpI_p2 | atpH-atpI | AATAACGGAAGCGGCAGAAA |
TCTATGGAGGGACATCATTGA |
1292–1358 | 1.000 | 62.5 |
| atpH-atpI_p3 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
ATCTATGGAGGGACATCATTGA |
1292–1358 | 1.000 | 60.2 |
| atpH-atpI_p4 | atpH-atpI | AATAACGGAAGCGGCAGAAA |
ATCTATGGAGGGACATCATTGA |
1293–1359 | 1.000 | 59.0 |
| atpH-atpI_p5 | atpH-atpI | TAACGGAAGCGGCAGAAATC |
TCTATGGAGGGACATCATTGA |
1290–1356 | 1.000 | 58.9 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | ATTCCCGCATTTCCATCTCC |
AAAAGGATTTGCAGTCCCCC |
1174–1372 | 1.000 | 88.5 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | ATTCCCGCATTTCCATCTCC |
ATCGTTTGTTGATCAGGCGA |
1215–1413 | 0.935 | 87.8 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | ATTCCCGCATTTCCATCTCC |
GCGACACCCAGATTTGAACT |
1199–1397 | 1.000 | 87.4 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | ATTCCCGCATTTCCATCTCC |
GTTTGTTGATCAGGCGACAC |
1212–1410 | 0.935 | 86.0 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | GCATTTCCATCTCCGAGCAT |
ATCGTTTGTTGATCAGGCGA |
1209–1407 | 0.935 | 84.7 |
Result downloads
Reference species (31)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Zanthoxylum acanthopodium | NC_051878.1 | 158473 | View on NCBI ↗ |
| Zanthoxylum asiaticum | NC_056094.1 | 158434 | View on NCBI ↗ |
| Zanthoxylum austrosinense | NC_066646.1 | 158427 | View on NCBI ↗ |
| Zanthoxylum avicennae | NC_062045.1 | 158568 | View on NCBI ↗ |
| Zanthoxylum bungeanum | NC_031386.1 | 158401 | View on NCBI ↗ |
| Zanthoxylum bungeanum var. punctatum | MW246146.1 | 158776 | View on NCBI ↗ |
| Zanthoxylum calcicola | NC_053779.1 | 158591 | View on NCBI ↗ |
| Zanthoxylum dimorphophyllum | NC_068580.1 | 158458 | View on NCBI ↗ |
| Zanthoxylum dimorphophyllum var. spinifolium | MW478806.1 | 158458 | View on NCBI ↗ |
| Zanthoxylum esquirolii | NC_058996.1 | 158390 | View on NCBI ↗ |
| Zanthoxylum holtzianum | PV658283.1 | 158158 | View on NCBI ↗ |
| Zanthoxylum madagascariense | NC_046744.1 | 158071 | View on NCBI ↗ |
| Zanthoxylum micranthum | NC_066647.1 | 158805 | View on NCBI ↗ |
| Zanthoxylum multijugum | NC_053778.1 | 158578 | View on NCBI ↗ |
| Zanthoxylum nitidum | NC_050306.1 | 157307 | View on NCBI ↗ |
| Zanthoxylum nitidum var. nitidum | MN241095.1 | 157349 | View on NCBI ↗ |
| Zanthoxylum nitidum var. tomentosum | MN241098.1 | 157013 | View on NCBI ↗ |
| Zanthoxylum oxyphyllum | NC_053776.1 | 158316 | View on NCBI ↗ |
| Zanthoxylum paniculatum | NC_046745.1 | 158265 | View on NCBI ↗ |
| Zanthoxylum paracanthum | PV658284.1 | 157683 | View on NCBI ↗ |
| Zanthoxylum piasezkii | NC_053775.1 | 158393 | View on NCBI ↗ |
| Zanthoxylum pinnatum | NC_046746.1 | 158722 | View on NCBI ↗ |
| Zanthoxylum piperitum | NC_027939.1 | 158154 | View on NCBI ↗ |
| Zanthoxylum scandens | NC_066648.1 | 158503 | View on NCBI ↗ |
| Zanthoxylum schinifolium | NC_030702.1 | 158963 | View on NCBI ↗ |
| Zanthoxylum simulans | NC_037482.1 | 158461 | View on NCBI ↗ |
| Zanthoxylum stenophyllum | NC_058754.1 | 158314 | View on NCBI ↗ |
| Zanthoxylum stipitatum | NC_056315.1 | 158752 | View on NCBI ↗ |
| Zanthoxylum tragodes | NC_046747.1 | 158425 | View on NCBI ↗ |
| Zanthoxylum undulatifolium | NC_058995.1 | 158400 | View on NCBI ↗ |
| Zanthoxylum usambarense | PQ459007.1 | 157790 | View on NCBI ↗ |