| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16 | LSC | 1163 | 0.0044 | 0.98 | 40.9 | yes | View details |
| rps16-trnQ-UUG | LSC | 1021 | 0.0059 | 0.95 | 54.6 | yes | View details |
| trnT-GGU-psbD | LSC | 1175 | 0.0090 | 0.96 | 50.2 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 511 | 0.0105 | 0.98 | 45.6 | yes | View details |
| petA-psbJ | LSC | 796 | 0.0082 | 0.99 | 65.6 | yes | View details |
| rrn5-trnR-ACG | IRb | 283 | 0.0196 | 0.91 | 58.4 | yes | View details |
| trnR-ACG-trnN-GUU | IRb | 465 | 0.0023 | 1.00 | 44.2 | yes | View details |
| trnL-UAG-rpl32 | SSC | 856 | 0.0131 | 0.96 | 75.8 | yes | View details |
| rpl32-ndhF | SSC | 1063 | 0.0117 | 0.91 | 57.9 | yes | View details |
| rps19-trnH-GUG | IRa | 2 | 0.0000 | 0.99 | 70.9 | no | View details |
| ndhF-ycf1 | SSC | 42 | 0.0465 | 1.00 | 65.4 | yes | View details |
| trnK-UUU-rps16 | LSC | 820 | 0.0037 | 0.96 | 58.5 | yes | View details |
| psbA-trnK-UUU | LSC | 204 | 0.0110 | 0.94 | 58.3 | yes | View details |
| psbM-trnD-GUC | LSC | 648 | 0.0045 | 0.98 | 57.6 | yes | View details |
| trnY-GUA-rpoB | LSC | 1087 | 0.0041 | 0.95 | 57.1 | yes | View details |
| accD-psaI | LSC | 729 | 0.0065 | 0.98 | 56.6 | yes | View details |
| trnH-GUG-psbA | LSC | 407 | 0.0062 | 0.97 | 56.5 | yes | View details |
| rpl16-rps3 | LSC | 1216 | 0.0058 | 0.97 | 55.6 | 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
27
Genome length
151–152 kb
Candidate markers
265
Primer pairs
85
Genome-wide nucleotide diversity
Candidate markers
9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).
Primer pairs
Showing the top 30 of 85 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 |
CCGTGCTAACCTTGGTATGG |
377–584 | 1.000 | 82.9 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
CCGTGCTAACCTTGGTATGG |
391–598 | 1.000 | 82.8 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
CCGTGCTAACCTTGGTATGG |
390–597 | 1.000 | 82.8 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
CCGTGCTAACCTTGGTATGG |
392–599 | 1.000 | 82.7 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
ACCGTGCTAACCTTGGTATG |
378–585 | 1.000 | 82.4 |
| psbA-trnK-UUU_p1 | psbA-trnK-UUU | ACGCCAAACCATCCAATGTA |
CTAGTTCCGGGTTCGAATCC |
326–339 | 1.000 | 86.9 |
| psbA-trnK-UUU_p2 | psbA-trnK-UUU | TAAAGACGGTTTTCGGTGCT |
GAAAGCCGTGTGCAATGAAA |
393–406 | 1.000 | 86.3 |
| psbA-trnK-UUU_p3 | psbA-trnK-UUU | ACGCCAAACCATCCAATGTA |
GAAAGCCGTGTGCAATGAAA |
411–424 | 1.000 | 86.2 |
| psbA-trnK-UUU_p4 | psbA-trnK-UUU | AGGGATCATCAAAACGCCAA |
GAAAGCCGTGTGCAATGAAA |
424–437 | 1.000 | 85.9 |
| psbA-trnK-UUU_p5 | psbA-trnK-UUU | CAAAACGCCAAACCATCCAA |
GAAAGCCGTGTGCAATGAAA |
415–428 | 1.000 | 85.9 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | CCGATGGTATGGACGAATCC |
TTCCTTGAAAAAGGCGCTCA |
683–1017 | 1.000 | 83.5 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
TTCCTTGAAAAAGGCGCTCA |
622–956 | 1.000 | 82.9 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
TTCCTTGAAAAAGGCGCTCA |
621–955 | 1.000 | 82.9 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | TCCTAGCCGCACTTAAAAGC |
TTCCTTGAAAAAGGCGCTCA |
637–971 | 1.000 | 82.1 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | CCGCACTTAAAAGCCGAGTA |
TTCCTTGAAAAAGGCGCTCA |
631–965 | 1.000 | 82.0 |
| rps16_p1 | rps16 | AGCAAGAAAATAAGTAGAGCAAGAA |
GGTTCGAAATTAGAGGAATGT |
1268–1302 | 0.963 | 43.2 |
| rps16_p2 | rps16 | AGCAAGAAAATAAGTAGAGCAAGA |
GGTTCGAAATTAGAGGAATGT |
1284–1302 | 0.926 | 40.2 |
| rps16_p3 | rps16 | AGCAAGAAAATAAGTAGAGCAAGA |
GGTTCGAAATTAGAGGAATGTT |
1284–1302 | 0.926 | 40.2 |
| rps16_p4 | rps16 | GCAAGAAAATAAGTAGAGCAAGA |
GGTTCGAAATTAGAGGAATGT |
1283–1301 | 0.926 | 40.2 |
| rps16_p5 | rps16 | AGCAAGAAAATAAGTAGAGCAAG |
GGTTCGAAATTAGAGGAATGT |
1284–1302 | 0.926 | 40.2 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
GAGGTTCGAATCCTTCCGTC |
1061–1112 | 1.000 | 86.9 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1044–1095 | 1.000 | 86.5 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | CAACGGATCGTGTCCTTCAA |
GAGGTTCGAATCCTTCCGTC |
1062–1113 | 1.000 | 85.9 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | CGGATCGTGTCCTTCAAGTC |
GAGGTTCGAATCCTTCCGTC |
1059–1110 | 1.000 | 84.6 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | GGATCGTGTCCTTCAAGTCG |
GAGGTTCGAATCCTTCCGTC |
1058–1109 | 1.000 | 84.6 |
| psbM-trnD-GUC_p1 | psbM-trnD-GUC | TTGACTGGCTGTTTTTACGT |
TTCAATAGGCAAGAGCACCG |
795–821 | 1.000 | 65.2 |
| psbM-trnD-GUC_p2 | psbM-trnD-GUC | TTTGACTGGCTGTTTTTACGT |
TTCAATAGGCAAGAGCACCG |
796–822 | 1.000 | 63.3 |
| psbM-trnD-GUC_p3 | psbM-trnD-GUC | TTTTGACTGGCTGTTTTTACGT |
TTCAATAGGCAAGAGCACCG |
797–823 | 1.000 | 61.0 |
| psbM-trnD-GUC_p4 | psbM-trnD-GUC | TGACTGGCTGTTTTTACGTA |
TTCAATAGGCAAGAGCACCG |
794–820 | 1.000 | 58.2 |
| psbM-trnD-GUC_p5 | psbM-trnD-GUC | TTGACTGGCTGTTTTTACGT |
GTTCAATAGGCAAGAGCACC |
796–822 | 1.000 | 57.5 |
Result downloads
Reference species (27)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Bidens alba var. radiata | NC_047269.1 | 151653 | View on NCBI ↗ |
| Bidens amplectens | NC_047267.1 | 151765 | View on NCBI ↗ |
| Bidens asymmetrica | NC_047268.1 | 151856 | View on NCBI ↗ |
| Bidens campylotheca subsp. campylotheca | NC_047253.1 | 151788 | View on NCBI ↗ |
| Bidens campylotheca subsp. pentamera | NC_047270.1 | 151805 | View on NCBI ↗ |
| Bidens cervicata | NC_047264.1 | 151831 | View on NCBI ↗ |
| Bidens conjuncta | NC_047263.1 | 151714 | View on NCBI ↗ |
| Bidens cosmoides | NC_047278.1 | 151818 | View on NCBI ↗ |
| Bidens forbesii subsp. forbesii | NC_047252.1 | 151660 | View on NCBI ↗ |
| Bidens forbesii subsp. kahiliensis | NC_047258.1 | 151808 | View on NCBI ↗ |
| Bidens hawaiensis | NC_047259.1 | 151680 | View on NCBI ↗ |
| Bidens hillebrandiana subsp. polycephala | NC_046893.1 | 151798 | View on NCBI ↗ |
| Bidens macrocarpa | NC_047274.1 | 151774 | View on NCBI ↗ |
| Bidens mauiensis | NC_047254.1 | 151826 | View on NCBI ↗ |
| Bidens menziesii subsp. filiformis | NC_047273.1 | 151791 | View on NCBI ↗ |
| Bidens menziesii subsp. filiformis x Bidens micrantha subsp. ctenophylla | NC_047260.1 | 151674 | View on NCBI ↗ |
| Bidens micrantha subsp. ctenophylla | NC_047277.1 | 151665 | View on NCBI ↗ |
| Bidens micrantha subsp. kalealaha | NC_047266.1 | 151687 | View on NCBI ↗ |
| Bidens molokaiensis | NC_047261.1 | 151710 | View on NCBI ↗ |
| Bidens pachyloma | NC_047272.1 | 151284 | View on NCBI ↗ |
| Bidens sandvicensis | NC_047276.1 | 151794 | View on NCBI ↗ |
| Bidens sandvicensis subsp. confusa | NC_047255.1 | 151730 | View on NCBI ↗ |
| Bidens sandvicensis subsp. sandvicensis | NC_047257.1 | 151739 | View on NCBI ↗ |
| Bidens schimperi | NC_047271.1 | 150932 | View on NCBI ↗ |
| Bidens torta | NC_047275.1 | 151807 | View on NCBI ↗ |
| Bidens valida | NC_047256.1 | 151722 | View on NCBI ↗ |
| Bidens wiebkei | NC_047262.1 | 151688 | View on NCBI ↗ |