| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnT-UGU-trnL-UAA | LSC | 663 | 0.0166 | 1.00 | 62.6 | yes | View details |
| petA-psbJ | LSC | 1029 | 0.0180 | 1.00 | 74.7 | yes | View details |
| ndhF | SSC | 2223 | 0.0111 | 1.00 | 55.0 | yes | View details |
| ndhF-rpl32 | SSC | 505 | 0.0165 | 1.00 | 64.5 | yes | View details |
| ccsA | SSC | 972 | 0.0098 | 1.00 | 49.4 | yes | View details |
| rps15 | SSC | 336 | 0.0120 | 1.00 | 44.7 | yes | View details |
| ycf1 | SSC | 5493 | 0.0139 | 1.00 | 58.7 | yes | View details |
| trnH-GUG-psbA | LSC | 230 | 0.0274 | 1.00 | 74.2 | yes | View details |
| ycf4-cemA | LSC | 559 | 0.0109 | 1.00 | 68.9 | yes | View details |
| psaA-ycf3 | LSC | 727 | 0.0085 | 0.99 | 67.3 | yes | View details |
| trnK-UUU-rps16 | LSC | 914 | 0.0124 | 1.00 | 66.0 | yes | View details |
| rps16-trnQ-UUG | LSC | 993 | 0.0134 | 0.99 | 65.3 | yes | View details |
| rpoB-trnC-GCA | LSC | 1096 | 0.0110 | 1.00 | 65.2 | yes | View details |
| trnT-GGU-psbD | LSC | 1247 | 0.0090 | 1.00 | 65.1 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 557 | 0.0143 | 1.00 | 64.5 | yes | View details |
| rpl32-trnL-UAG | SSC | 526 | 0.0172 | 1.00 | 64.5 | yes | View details |
| ndhC-trnV-UAC | LSC | 954 | 0.0134 | 1.00 | 64.4 | 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
47
Genome length
151–152 kb
Candidate markers
270
Primer pairs
85
Genome-wide nucleotide diversity
Candidate markers
7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 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 |
CAACCGTGCTAACCTTGGTA |
320–372 | 1.000 | 89.6 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
CAACCGTGCTAACCTTGGTA |
334–386 | 1.000 | 89.6 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
CAACCGTGCTAACCTTGGTA |
333–385 | 1.000 | 89.5 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
CAACCGTGCTAACCTTGGTA |
335–387 | 1.000 | 89.5 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
ATCAACCGTGCTAACCTTGG |
322–374 | 1.000 | 89.5 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AAAGCCGAGTACTCTACCGT |
AGGAACTTCCGCCTAATCAA |
970–1029 | 1.000 | 78.6 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
AGGAACTTCCGCCTAATCAA |
969–1028 | 1.000 | 78.6 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | TCTAGCCGCACTTAAAAGCC |
AGGAACTTCCGCCTAATCAA |
984–1043 | 1.000 | 77.7 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | CCGCACTTAAAAGCCGAGTA |
AGGAACTTCCGCCTAATCAA |
979–1038 | 1.000 | 77.6 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | AAGCCGAGTACTCTACCGTT |
AGGAACTTCCGCCTAATCAAA |
969–1028 | 1.000 | 76.7 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
GAAATTGAAATGGGGCGTGG |
817–1150 | 1.000 | 90.8 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
TGACTGGCATAACATCCACG |
1276–1603 | 1.000 | 90.2 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
AGCAGCTTGCCAAACAAAAG |
1320–1647 | 1.000 | 89.8 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
CTTACAGCAGCTTGCCAAAC |
1325–1652 | 1.000 | 89.7 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AACGGATCGTGTCCTTCAAG |
CGTGTGAATCGAGGGTTCAT |
1442–1770 | 0.957 | 88.0 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
ACGAATCACACTTTTACCACT |
622–637 | 1.000 | 62.2 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
ACGAATCACACTTTTACCACT |
621–636 | 1.000 | 62.2 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
AGAACGAATCACACTTTTACCAC |
625–640 | 1.000 | 61.1 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
GAACGAATCACACTTTTACCACT |
624–639 | 1.000 | 61.1 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
GAACGAATCACACTTTTACCACT |
623–638 | 1.000 | 61.1 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | CATTGCCTCATTTGCATCCC |
CCGGATTTGAACTGGGGAAA |
1094–1209 | 1.000 | 88.1 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | CATTGCCTCATTTGCATCCC |
TTTGGTAATGAGGCGACACC |
1113–1228 | 1.000 | 87.3 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | CATTGCCTCATTTGCATCCC |
AAAAGGATTTGCAGTCCCCC |
1076–1191 | 1.000 | 86.1 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | ATTGCCTCATTTGCATCCCC |
CCGGATTTGAACTGGGGAAA |
1093–1208 | 1.000 | 83.0 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | ACATTGCCTCATTTGCATCC |
CCGGATTTGAACTGGGGAAA |
1095–1210 | 1.000 | 82.2 |
| trnT-GGU-psbD_p1 | trnT-GGU-psbD | GTGGTAGAGTAACGCCATGG |
ACAAAAACGAAACGGTCCCT |
1342–1420 | 1.000 | 87.4 |
| trnT-GGU-psbD_p2 | trnT-GGU-psbD | TCAGTGGTAGAGTAACGCCA |
ACAAAAACGAAACGGTCCCT |
1345–1423 | 1.000 | 87.2 |
| trnT-GGU-psbD_p3 | trnT-GGU-psbD | ATAGTGACTCGTCCGGGAAT |
ACAAAAACGAAACGGTCCCT |
1388–1466 | 0.979 | 86.6 |
| trnT-GGU-psbD_p4 | trnT-GGU-psbD | GTGGTAGAGTAACGCCATGG |
CAAAAACGAAACGGTCCCTC |
1341–1419 | 0.957 | 84.1 |
| trnT-GGU-psbD_p5 | trnT-GGU-psbD | ATAGTGACTCGTCCGGGAAT |
CAAAAACGAAACGGTCCCTC |
1387–1465 | 0.936 | 83.4 |
Result downloads
Reference species (47)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Phlomoides adylovii | NC_085511.1 | 151760 | View on NCBI ↗ |
| Phlomoides anisochila | PV929680.1 | 151509 | View on NCBI ↗ |
| Phlomoides atropurpurea | NC_085451.1 | 151841 | View on NCBI ↗ |
| Phlomoides baissunensis | NC_085448.1 | 151359 | View on NCBI ↗ |
| Phlomoides brachystegia | NC_085431.1 | 151482 | View on NCBI ↗ |
| Phlomoides breviflora | NC_085429.1 | 151856 | View on NCBI ↗ |
| Phlomoides canescens | NC_085440.1 | 151843 | View on NCBI ↗ |
| Phlomoides chinghoensis | NC_085512.1 | 151844 | View on NCBI ↗ |
| Phlomoides codonantha | NC_085454.1 | 151298 | View on NCBI ↗ |
| Phlomoides congesta | NC_085513.1 | 151871 | View on NCBI ↗ |
| Phlomoides cordifolia | NC_085432.1 | 151572 | View on NCBI ↗ |
| Phlomoides deserticola | NC_085441.1 | 151510 | View on NCBI ↗ |
| Phlomoides ebracteolata | NC_085439.1 | 151363 | View on NCBI ↗ |
| Phlomoides eremostachydioides | NC_085426.1 | 151585 | View on NCBI ↗ |
| Phlomoides franchetiana | NC_085452.1 | 151927 | View on NCBI ↗ |
| Phlomoides hamosa | NC_061415.1 | 151738 | View on NCBI ↗ |
| Phlomoides isochila | PX921649.1 | 151538 | View on NCBI ↗ |
| Phlomoides kermanica | NC_085449.1 | 151348 | View on NCBI ↗ |
| Phlomoides kirghisorum | NC_067634.1 | 151563 | View on NCBI ↗ |
| Phlomoides labiosa | NC_085427.1 | 151284 | View on NCBI ↗ |
| Phlomoides labiosiformis | NC_085453.1 | 151327 | View on NCBI ↗ |
| Phlomoides labiosissima | NC_085445.1 | 151327 | View on NCBI ↗ |
| Phlomoides laciniata | NC_085430.1 | 151334 | View on NCBI ↗ |
| Phlomoides lehmanniana | NC_085447.1 | 151114 | View on NCBI ↗ |
| Phlomoides longiaristata | NC_085514.1 | 151763 | View on NCBI ↗ |
| Phlomoides megalantha | NC_085356.1 | 151519 | View on NCBI ↗ |
| Phlomoides molucelloides | NC_085443.1 | 151524 | View on NCBI ↗ |
| Phlomoides nuda | NC_085444.1 | 151524 | View on NCBI ↗ |
| Phlomoides ornata | NC_085357.1 | 151905 | View on NCBI ↗ |
| Phlomoides pedunculata | NC_085442.1 | 152010 | View on NCBI ↗ |
| Phlomoides pratensis | NC_085515.1 | 151844 | View on NCBI ↗ |
| Phlomoides puberula | NC_085434.1 | 151761 | View on NCBI ↗ |
| Phlomoides sagittata | NC_085508.1 | 151784 | View on NCBI ↗ |
| Phlomoides sarawschanica | NC_085435.1 | 151323 | View on NCBI ↗ |
| Phlomoides sewerzovii | NC_085437.1 | 151587 | View on NCBI ↗ |
| Phlomoides sogdiana | NC_085516.1 | 151511 | View on NCBI ↗ |
| Phlomoides speciosa | NC_085438.1 | 151288 | View on NCBI ↗ |
| Phlomoides subspicata | NC_085517.1 | 151335 | View on NCBI ↗ |
| Phlomoides szechuanensis | NC_085358.1 | 151953 | View on NCBI ↗ |
| Phlomoides tatsienensis | NC_085359.1 | 151899 | View on NCBI ↗ |
| Phlomoides thyrsiflora | NC_085428.1 | 151330 | View on NCBI ↗ |
| Phlomoides transoxana | NC_085436.1 | 151531 | View on NCBI ↗ |
| Phlomoides tuberosa | NC_085518.1 | 151764 | View on NCBI ↗ |
| Phlomoides tuvinica | NC_085433.1 | 151766 | View on NCBI ↗ |
| Phlomoides umbrosa | NC_061394.1 | 152008 | View on NCBI ↗ |
| Phlomoides younghusbandii | PP234524.1 | 151777 | View on NCBI ↗ |
| Phlomoides zenaidae | NC_085450.1 | 151596 | View on NCBI ↗ |