| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnK-UUU-rps16 | LSC | 791 | 0.0128 | 0.97 | 61.2 | yes | View details |
| rpoB-trnC-GCA | LSC | 1132 | 0.0066 | 1.00 | 47.9 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 647 | 0.0065 | 1.00 | 60.8 | yes | View details |
| psbC-trnS-UGA | LSC | 226 | 0.0305 | 1.00 | 71.6 | yes | View details |
| trnS-UGA-psbZ | LSC | 378 | 0.0080 | 1.00 | 42.7 | yes | View details |
| ycf3-trnS-GGA | LSC | 825 | 0.0066 | 0.99 | 54.6 | yes | View details |
| rps4-trnT-UGU | LSC | 369 | 0.0047 | 0.98 | 39.5 | yes | View details |
| trnV-UAC-trnM-CAU | LSC | 194 | 0.0004 | 1.00 | 26.2 | yes | View details |
| rbcL-psaI | LSC | 1310 | 0.0050 | 0.99 | 63.4 | yes | View details |
| petD | LSC | 1218 | 0.0068 | 1.00 | 47.0 | yes | View details |
| ndhF-rpl32 | SSC | 666 | 0.0065 | 0.98 | 56.3 | yes | View details |
| trnR-UCU-atpA | LSC | 76 | 0.0306 | 0.91 | 59.0 | yes | View details |
| trnM-CAU-atpE | LSC | 174 | 0.0211 | 1.00 | 58.1 | yes | View details |
| trnT-GGU-psbD | LSC | 1156 | 0.0022 | 1.00 | 56.6 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 592 | 0.0058 | 0.99 | 56.4 | yes | View details |
| trnH-GUG-psbA | LSC | 264 | 0.0100 | 1.00 | 56.3 | yes | View details |
| atpH-atpI | LSC | 1090 | 0.0019 | 1.00 | 55.0 | yes | View details |
| ycf1 | SSC | 5343 | 0.0027 | 1.00 | 54.6 | yes | View details |
| psbE-petL | LSC | 966 | 0.0048 | 0.99 | 54.0 | yes | View details |
| ndhA | SSC | 2188 | 0.0017 | 1.00 | 52.4 | yes | View details |
| ycf1 | IRb | 1107 | 0.0001 | 0.99 | 46.5 | no | 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
147–149 kb
Candidate markers
266
Primer pairs
100
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 266 candidates).
Primer pairs
Showing the top 30 of 100 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 |
CAACCGTGCTAACCTTGGTA |
378–414 | 1.000 | 84.4 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
ATCAACCGTGCTAACCTTGG |
380–416 | 1.000 | 84.4 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
CAACCGTGCTAACCTTGGTA |
392–428 | 1.000 | 84.3 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
CAACCGTGCTAACCTTGGTA |
391–427 | 1.000 | 84.3 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
CAACCGTGCTAACCTTGGTA |
393–429 | 1.000 | 84.3 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | CCGATGGTATGGACGAATCC |
GGTGCTCAACCTACAGGAAC |
948–997 | 1.000 | 85.1 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
GGTGCTCAACCTACAGGAAC |
887–936 | 1.000 | 84.6 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
GGTGCTCAACCTACAGGAAC |
886–935 | 1.000 | 84.6 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | CCGCACTTAAAAGCCGAGTA |
GGTGCTCAACCTACAGGAAC |
896–945 | 1.000 | 83.7 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | TGGACGAATCCTTCCCTTCA |
GGTGCTCAACCTACAGGAAC |
939–988 | 1.000 | 83.0 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | ATTAGCAATCCGCCGCTTTA |
TGAATCAAACCGAAAGACCCT |
661–957 | 1.000 | 73.3 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
TGAATCAAACCGAAAGACCCT |
710–1006 | 1.000 | 72.4 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | ACAACAACGGAAAGAGAGGG |
TGAATCAAACCGAAAGACCCT |
716–1012 | 1.000 | 71.5 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | GCTTTAGTCCACTCAGCCAT |
TGAATCAAACCGAAAGACCCT |
647–943 | 1.000 | 70.4 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AGTCCACTCAGCCATCTCTC |
TGAATCAAACCGAAAGACCCT |
642–938 | 1.000 | 69.6 |
| trnR-UCU-atpA_p1 | trnR-UCU-atpA | TGGGCGTCCATTGTCTAATG |
GACATTTACTAAGGACGCGGA |
225–243 | 1.000 | 76.5 |
| trnR-UCU-atpA_p2 | trnR-UCU-atpA | TGGGCGTCCATTGTCTAATG |
AGACATTTACTAAGGACGCGG |
226–244 | 1.000 | 76.5 |
| trnR-UCU-atpA_p3 | trnR-UCU-atpA | TGGGCGTCCATTGTCTAATG |
ACATTTACTAAGGACGCGGA |
224–242 | 1.000 | 75.1 |
| trnR-UCU-atpA_p4 | trnR-UCU-atpA | TGGGCGTCCATTGTCTAATG |
ACATTTACTAAGGACGCGGAA |
224–242 | 1.000 | 73.0 |
| trnR-UCU-atpA_p5 | trnR-UCU-atpA | TGGGCGTCCATTGTCTAATG |
GACATTTACTAAGGACGCGG |
225–243 | 1.000 | 72.6 |
| atpH-atpI_p1 | atpH-atpI | AACAGAAGCGGCAGAAATCA |
TTTTGCAACTTTAGCTGCGG |
1170–1234 | 1.000 | 83.1 |
| atpH-atpI_p2 | atpH-atpI | AACAGAAGCGGCAGAAATCA |
TAGCTGCGGCGTATATAGGT |
1159–1223 | 1.000 | 82.9 |
| atpH-atpI_p3 | atpH-atpI | AGCCAATCCAGCAGCAATAA |
TTTTGCAACTTTAGCTGCGG |
1188–1252 | 1.000 | 82.7 |
| atpH-atpI_p4 | atpH-atpI | TACCCTCTACAGCTTGACCC |
TTTTGCAACTTTAGCTGCGG |
1255–1319 | 1.000 | 82.5 |
| atpH-atpI_p5 | atpH-atpI | GCGATACCCTCTACAGCTTG |
TTTTGCAACTTTAGCTGCGG |
1259–1323 | 1.000 | 82.5 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | CGAGCCCATATCCTTGCTTT |
AGGCAATAATTCGGCGAGTT |
1772–1807 | 1.000 | 85.2 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | TGTTCTTGCATATCCCTGCC |
AGGCAATAATTCGGCGAGTT |
1550–1585 | 1.000 | 85.2 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | CCGGGGCTTTGCAATATTTG |
AGGCAATAATTCGGCGAGTT |
1652–1687 | 1.000 | 85.1 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | CGAGCCCATATCCTTGCTTT |
CCGGATTTGAACTGGGGAAA |
1697–1728 | 1.000 | 84.9 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | CGAGCCCATATCCTTGCTTT |
CTATACAAACCCCACCCAGC |
1842–1885 | 0.893 | 80.7 |
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 |
|---|---|---|---|
| Trigonotis amblyosepala | NC_070038.1 | 147506 | View on NCBI ↗ |
| Trigonotis barkamensis | NC_070020.1 | 148564 | View on NCBI ↗ |
| Trigonotis bracteata | NC_070021.1 | 148013 | View on NCBI ↗ |
| Trigonotis cavaleriei | NC_070022.1 | 147645 | View on NCBI ↗ |
| Trigonotis cinereifolia | NC_070023.1 | 148986 | View on NCBI ↗ |
| Trigonotis coreana | NC_070024.1 | 148480 | View on NCBI ↗ |
| Trigonotis corispermoides | NC_070025.1 | 148402 | View on NCBI ↗ |
| Trigonotis delicatula | NC_070026.1 | 148719 | View on NCBI ↗ |
| Trigonotis floribunda | NC_070027.1 | 148698 | View on NCBI ↗ |
| Trigonotis formosana var. elevatovenosa | ON620186.1 | 148439 | View on NCBI ↗ |
| Trigonotis giraldii | NC_070028.1 | 148084 | View on NCBI ↗ |
| Trigonotis gracilipes | NC_070029.1 | 148489 | View on NCBI ↗ |
| Trigonotis heliotropifolia | NC_070030.1 | 148641 | View on NCBI ↗ |
| Trigonotis laxa | NC_070031.1 | 148658 | View on NCBI ↗ |
| Trigonotis leucantha | NC_070032.1 | 148587 | View on NCBI ↗ |
| Trigonotis microcarpa | NC_070033.1 | 148512 | View on NCBI ↗ |
| Trigonotis mollis | NC_070034.1 | 147513 | View on NCBI ↗ |
| Trigonotis motuoensis | NC_070035.1 | 148667 | View on NCBI ↗ |
| Trigonotis omeiensis | NC_070036.1 | 148671 | View on NCBI ↗ |
| Trigonotis peduncularis | NC_070037.1 | 147500 | View on NCBI ↗ |
| Trigonotis peduncularis var. macrantha | ON620203.1 | 147487 | View on NCBI ↗ |
| Trigonotis petiolaris | NC_070039.1 | 148462 | View on NCBI ↗ |
| Trigonotis radicans | NC_070040.1 | 148595 | View on NCBI ↗ |
| Trigonotis rockii | NC_070041.1 | 148281 | View on NCBI ↗ |
| Trigonotis tenera | NC_070042.1 | 147851 | View on NCBI ↗ |
| Trigonotis tibetica | NC_070043.1 | 148193 | View on NCBI ↗ |
| Trigonotis vestita | NC_070044.1 | 147904 | View on NCBI ↗ |
| Trigonotis zhuokejiensis | NC_070045.1 | 148575 | View on NCBI ↗ |