| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnK-UUU-rps16 | LSC | 890 | 0.0155 | 0.99 | 70.3 | yes | View details |
| rps16-trnQ-UUG | LSC | 1116 | 0.0163 | 0.99 | 73.1 | yes | View details |
| trnC-GCA-petN | LSC | 841 | 0.0126 | 1.00 | 68.6 | yes | View details |
| ndhF | SSC | 2256 | 0.0075 | 1.00 | 46.9 | yes | View details |
| ndhF-rpl32 | SSC | 506 | 0.0157 | 1.00 | 65.4 | yes | View details |
| rpl32-trnL-UAG | SSC | 898 | 0.0203 | 1.00 | 71.6 | yes | View details |
| ycf1 | SSC | 5406 | 0.0105 | 1.00 | 54.9 | yes | View details |
| ndhC-trnV-UAC | LSC | 1151 | 0.0102 | 1.00 | 72.8 | yes | View details |
| ccsA-ndhD | SSC | 240 | 0.0209 | 0.98 | 69.6 | yes | View details |
| petA-psbJ | LSC | 934 | 0.0092 | 1.00 | 69.2 | yes | View details |
| ycf4-cemA | LSC | 874 | 0.0075 | 1.00 | 67.3 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 702 | 0.0079 | 1.00 | 64.2 | yes | View details |
| ndhD-psaC | SSC | 124 | 0.0350 | 1.00 | 64.2 | yes | View details |
| psbZ-trnG-GCC | LSC | 304 | 0.0161 | 0.96 | 63.2 | yes | View details |
| trnT-GGU-psbD | LSC | 1347 | 0.0081 | 1.00 | 63.0 | yes | View details |
| ycf3-trnS-GGA | LSC | 831 | 0.0074 | 1.00 | 61.8 | 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
28
Genome length
154–154 kb
Candidate markers
270
Primer pairs
80
Genome-wide nucleotide diversity
Candidate markers
7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).
Primer pairs
Showing the top 30 of 80 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 |
GGAACTTCCGTCTAATCAAACG |
944–974 | 1.000 | 69.0 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
GGAACTTCCGTCTAATCAAACG |
943–973 | 1.000 | 69.0 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | TCTAGCCGCACTTAAAAGCC |
GGAACTTCCGTCTAATCAAACG |
958–988 | 1.000 | 68.2 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | TCAGTCGTGGTCTTCCAAAC |
GGAACTTCCGTCTAATCAAACG |
1029–1059 | 1.000 | 67.8 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | CAGTCGTGGTCTTCCAAACT |
GGAACTTCCGTCTAATCAAACG |
1028–1058 | 1.000 | 67.7 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1161–1222 | 1.000 | 89.4 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAAATTGAAATGGGGCGTGG |
1219–1280 | 0.964 | 88.0 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | GGATCGTGTCCTTCAAGTCG |
GAGGTTCGAATCCTTCCGTC |
1175–1236 | 1.000 | 87.5 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | GGATCGTGTCCTTCAAGTCG |
GAAATTGAAATGGGGCGTGG |
1233–1294 | 0.964 | 86.0 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | CGTTGCTTTCTACCACATCG |
GAAATTGAAATGGGGCGTGG |
1211–1272 | 0.964 | 82.8 |
| trnC-GCA-petN_p1 | trnC-GCA-petN | TTTCCCCAGTTCAAATCCGG |
ACTTCTTCCCCACACTACGA |
913–956 | 1.000 | 88.5 |
| trnC-GCA-petN_p2 | trnC-GCA-petN | TTTCCCCAGTTCAAATCCGG |
TTCTTCCCCACACTACGAGT |
911–954 | 1.000 | 88.5 |
| trnC-GCA-petN_p3 | trnC-GCA-petN | TTTCCCCAGTTCAAATCCGG |
CACTTCTTCCCCACACTACG |
914–957 | 1.000 | 87.9 |
| trnC-GCA-petN_p4 | trnC-GCA-petN | TTGTATCAGTTTGGCGGCAT |
ACTTCTTCCCCACACTACGA |
967–1010 | 1.000 | 87.7 |
| trnC-GCA-petN_p5 | trnC-GCA-petN | TTGTATCAGTTTGGCGGCAT |
TTCTTCCCCACACTACGAGT |
965–1008 | 1.000 | 87.7 |
| trnT-GGU-psbD_p1 | trnT-GGU-psbD | GTGGTAGAGTAACGCCATGG |
ACAAAAACGAAACGGTCCCT |
1461–1521 | 1.000 | 84.0 |
| trnT-GGU-psbD_p2 | trnT-GGU-psbD | TCAGTGGTAGAGTAACGCCA |
ACAAAAACGAAACGGTCCCT |
1464–1524 | 1.000 | 83.8 |
| trnT-GGU-psbD_p3 | trnT-GGU-psbD | GTGGTAGAGTAACGCCATGG |
GGACCAGCCTACAAAAACGA |
1496–1531 | 0.964 | 81.5 |
| trnT-GGU-psbD_p4 | trnT-GGU-psbD | TCAGTGGTAGAGTAACGCCA |
GGACCAGCCTACAAAAACGA |
1499–1534 | 0.964 | 81.3 |
| trnT-GGU-psbD_p5 | trnT-GGU-psbD | GGCGTAAGTCATCGGTTCAA |
GGACCAGCCTACAAAAACGA |
1473–1508 | 0.964 | 79.8 |
| psbZ-trnG-GCC_p1 | psbZ-trnG-GCC | TTGCTTCTCCTGATGGTTGG |
AATCGAACCCGCATCTTCTC |
447–479 | 1.000 | 87.6 |
| psbZ-trnG-GCC_p2 | psbZ-trnG-GCC | TTGCTTCTCCTGATGGTTGG |
GAATCGAACCCGCATCTTCT |
448–480 | 1.000 | 87.5 |
| psbZ-trnG-GCC_p3 | psbZ-trnG-GCC | GCTTCTCCTGATGGTTGGTC |
AATCGAACCCGCATCTTCTC |
445–477 | 1.000 | 87.2 |
| psbZ-trnG-GCC_p4 | psbZ-trnG-GCC | GCTTCTCCTGATGGTTGGTC |
GAATCGAACCCGCATCTTCT |
446–478 | 1.000 | 87.2 |
| psbZ-trnG-GCC_p5 | psbZ-trnG-GCC | CCGTCGTATTTGCTTCTCCT |
AATCGAACCCGCATCTTCTC |
456–488 | 1.000 | 86.7 |
| ycf3-trnS-GGA_p1 | ycf3-trnS-GGA | TGCCTCCTTTTCTCCTGAAG |
CCCTCGGTAAACAAAAGCCT |
993–1026 | 1.000 | 76.8 |
| ycf3-trnS-GGA_p2 | ycf3-trnS-GGA | GCCTCCTTTTCTCCTGAAGT |
CCCTCGGTAAACAAAAGCCT |
992–1025 | 1.000 | 76.8 |
| ycf3-trnS-GGA_p3 | ycf3-trnS-GGA | TGCCTCCTTTTCTCCTGAAG |
ACGGAAAGAGAGGGATTCGA |
1014–1047 | 1.000 | 76.2 |
| ycf3-trnS-GGA_p4 | ycf3-trnS-GGA | GCCTCCTTTTCTCCTGAAGT |
ACGGAAAGAGAGGGATTCGA |
1013–1046 | 1.000 | 76.2 |
| ycf3-trnS-GGA_p5 | ycf3-trnS-GGA | TGCCTCCTTTTCTCCTGAAG |
TTCCAATGCTACGCCTTGAA |
964–997 | 1.000 | 76.1 |
Result downloads
Reference species (28)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Buddleja albiflora | NC_069922.1 | 154094 | View on NCBI ↗ |
| Buddleja alternifolia | NC_057238.1 | 154280 | View on NCBI ↗ |
| Buddleja americana | NC_069934.1 | 154199 | View on NCBI ↗ |
| Buddleja aromatica | NC_069935.1 | 154169 | View on NCBI ↗ |
| Buddleja asiatica | NC_069924.1 | 154161 | View on NCBI ↗ |
| Buddleja bhutanica | NC_069943.1 | 154189 | View on NCBI ↗ |
| Buddleja brachystachya | NC_069936.1 | 154240 | View on NCBI ↗ |
| Buddleja candida | NC_069926.1 | 154130 | View on NCBI ↗ |
| Buddleja caryopteridifolia | NC_069940.1 | 154333 | View on NCBI ↗ |
| Buddleja colvilei | NC_042766.1 | 154225 | View on NCBI ↗ |
| Buddleja crispa | NC_069923.1 | 154125 | View on NCBI ↗ |
| Buddleja curviflora | NC_069932.1 | 154328 | View on NCBI ↗ |
| Buddleja davidii | NC_069921.1 | 154111 | View on NCBI ↗ |
| Buddleja delavayi | NC_069937.1 | 154295 | View on NCBI ↗ |
| Buddleja fallowiana | NC_069925.1 | 154130 | View on NCBI ↗ |
| Buddleja forrestii | NC_069944.1 | 154137 | View on NCBI ↗ |
| Buddleja globosa | NC_068052.1 | 154034 | View on NCBI ↗ |
| Buddleja japonica | NC_069928.1 | 154184 | View on NCBI ↗ |
| Buddleja macrostachya | NC_069931.1 | 154122 | View on NCBI ↗ |
| Buddleja microstachya | NC_069938.1 | 154297 | View on NCBI ↗ |
| Buddleja myriantha | NC_069942.1 | 154198 | View on NCBI ↗ |
| Buddleja nivea | NC_069927.1 | 154151 | View on NCBI ↗ |
| Buddleja paniculata | NC_069929.1 | 154291 | View on NCBI ↗ |
| Buddleja salviifolia | NC_069933.1 | 154353 | View on NCBI ↗ |
| Buddleja sessilifolia | NC_042767.1 | 154202 | View on NCBI ↗ |
| Buddleja subcapitata | NC_069939.1 | 154273 | View on NCBI ↗ |
| Buddleja x wardii | NC_069941.1 | 154125 | View on NCBI ↗ |
| Buddleja yunnanensis | NC_069930.1 | 154223 | View on NCBI ↗ |