| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 320 | 0.0421 | 0.98 | 69.0 | yes | View details |
| rps16-trnQ-UUG | LSC | 1089 | 0.0212 | 0.99 | 63.5 | yes | View details |
| ycf1 | IRb | 864 | 0.0066 | 1.00 | 40.3 | no | View details |
| ccsA-ndhD | SSC | 241 | 0.0354 | 1.00 | 74.7 | yes | View details |
| rps15-ycf1 | SSC | 381 | 0.0225 | 1.00 | 48.9 | yes | View details |
| ycf1 | SSC | 5451 | 0.0200 | 1.00 | 56.1 | yes | View details |
| ndhC-trnV-UAC | LSC | 1061 | 0.0108 | 1.00 | 63.3 | yes | View details |
| trnT-GGU-psbD | LSC | 1336 | 0.0113 | 1.00 | 61.8 | yes | View details |
| rpoB-trnC-GCA | LSC | 1139 | 0.0102 | 0.95 | 61.7 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 696 | 0.0133 | 1.00 | 61.6 | yes | View details |
| rpl32-trnL-UAG | SSC | 867 | 0.0167 | 0.99 | 61.5 | yes | View details |
| ndhD-psaC | SSC | 100 | 0.0374 | 1.00 | 61.2 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 814 | 0.0160 | 0.98 | 59.0 | yes | View details |
| ycf4-cemA | LSC | 861 | 0.0095 | 1.00 | 58.7 | yes | View details |
| rpl20-rps12 | LSC | 824 | 0.0091 | 1.00 | 57.5 | yes | View details |
| trnG-UCC-trnR-UCU | LSC | 209 | 0.0254 | 1.00 | 57.0 | 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
24
Genome length
153–154 kb
Candidate markers
277
Primer pairs
75
Genome-wide nucleotide diversity
Candidate markers
6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 277 candidates).
Primer pairs
Showing the top 30 of 75 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 |
TCGAAGCTCCAACAAATG |
273–386 | 1.000 | 52.0 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
TCGAAGCTCCAACAAATG |
287–400 | 1.000 | 52.0 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
TCGAAGCTCCAACAAATG |
286–399 | 1.000 | 52.0 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
TCGAAGCTCCAACAAATG |
288–401 | 1.000 | 52.0 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | CGCATGGTGGATTCACAATC |
TCGAAGCTCCAACAAATG |
302–415 | 1.000 | 52.0 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AACGATGTCGAGACAAGAGC |
TGAAGCCACCCAATCACAAA |
1266–1584 | 1.000 | 90.2 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AACGATGTCGAGACAAGAGC |
TTGAAGCCACCCAATCACAA |
1267–1585 | 1.000 | 90.2 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AACGATGTCGAGACAAGAGC |
AGCAGCTTGCCAAACAAAAG |
1540–1856 | 1.000 | 89.6 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AACGATGTCGAGACAAGAGC |
CTTACAGCAGCTTGCCAAAC |
1545–1861 | 1.000 | 89.6 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | AACGATGTCGAGACAAGAGC |
GAGGTTCGAATCCTTCCGTC |
975–1293 | 0.792 | 81.3 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
ACGAATCACACTTTTACCACT |
855–896 | 1.000 | 59.7 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
ACGAATCACACTTTTACCACT |
854–895 | 1.000 | 59.7 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
AGAACGAATCACACTTTTACCAC |
858–899 | 1.000 | 58.6 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | CAATCCGACGCTTTAGTCCA |
GAACGAATCACACTTTTACCACT |
857–898 | 1.000 | 58.6 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AATCCGACGCTTTAGTCCAC |
GAACGAATCACACTTTTACCACT |
856–897 | 1.000 | 58.6 |
| trnG-UCC-trnR-UCU_p1 | trnG-UCC-trnR-UCU | TAACGATGCGGGTTCGATTC |
TGTCCTATCCATTAGACAATG |
256–267 | 1.000 | 49.8 |
| trnG-UCC-trnR-UCU_p2 | trnG-UCC-trnR-UCU | CTAACGATGCGGGTTCGATT |
TGTCCTATCCATTAGACAATG |
257–268 | 1.000 | 49.7 |
| trnG-UCC-trnR-UCU_p3 | trnG-UCC-trnR-UCU | AGCCTTCCAAGCTAACGATG |
TGTCCTATCCATTAGACAATG |
268–279 | 1.000 | 49.5 |
| trnG-UCC-trnR-UCU_p4 | trnG-UCC-trnR-UCU | CCTAGCCTTCCAAGCTAACG |
TGTCCTATCCATTAGACAATG |
271–282 | 1.000 | 49.5 |
| trnG-UCC-trnR-UCU_p5 | trnG-UCC-trnR-UCU | CCCTAGCCTTCCAAGCTAAC |
TGTCCTATCCATTAGACAATG |
272–283 | 1.000 | 49.4 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | ATTGCCTGATTTCCATCCCC |
CCGGATTTGAACTGGGGAAA |
1162–1229 | 0.958 | 85.3 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | ATTGCCTGATTTCCATCCCC |
AAAAGGATTTGCAGTCCCCC |
1144–1211 | 0.958 | 83.2 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | ATTGCCTGATTTCCATCCCC |
TTGTTTGATCAGGCGACACC |
1181–1248 | 0.958 | 79.7 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | ATTGCCTGATTTCCATCCCC |
GACACCCGGATTTGAACTGG |
1167–1234 | 0.958 | 79.2 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | CTGATTTCCATCCCCGAGC |
CCGGATTTGAACTGGGGAAA |
1157–1224 | 0.875 | 74.3 |
| trnE-UUC-trnT-GGU_p1 | trnE-UUC-trnT-GGU | TTTCGTAGTACCCTACCCCC |
GAACCGATGACTTACGCCTT |
753–948 | 1.000 | 86.2 |
| trnE-UUC-trnT-GGU_p2 | trnE-UUC-trnT-GGU | TTTCGTAGTACCCTACCCCC |
CCATGGCGTTACTCTACCAC |
732–927 | 1.000 | 85.9 |
| trnE-UUC-trnT-GGU_p3 | trnE-UUC-trnT-GGU | TTTCGTAGTACCCTACCCCC |
TGGCGTTACTCTACCACTGA |
729–924 | 1.000 | 85.7 |
| trnE-UUC-trnT-GGU_p4 | trnE-UUC-trnT-GGU | TTTCGTAGTACCCTACCCCC |
CCGATGACTTACGCCTTACC |
750–945 | 1.000 | 85.1 |
| trnE-UUC-trnT-GGU_p5 | trnE-UUC-trnT-GGU | TTTCGTAGTACCCTACCCCC |
GCGTTACTCTACCACTGAGC |
811 | 0.042 | 39.7 |
Result downloads
Reference species (24)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Lysionotus aeschynanthoides | PQ468968.1 | 153908 | View on NCBI ↗ |
| Lysionotus atropurpureus | PQ468986.1 | 153436 | View on NCBI ↗ |
| Lysionotus chatungii | PQ468991.1 | 153898 | View on NCBI ↗ |
| Lysionotus chingii | PQ468980.1 | 154278 | View on NCBI ↗ |
| Lysionotus denticulosus | PQ468966.1 | 154196 | View on NCBI ↗ |
| Lysionotus fengshanensis | PQ468979.1 | 154256 | View on NCBI ↗ |
| Lysionotus forrestii | PQ468993.1 | 153916 | View on NCBI ↗ |
| Lysionotus gamosepalus | PQ468978.1 | 153793 | View on NCBI ↗ |
| Lysionotus heterophyllus | PQ468967.1 | 153776 | View on NCBI ↗ |
| Lysionotus heterophyllus var. mollis | PQ468990.1 | 153710 | View on NCBI ↗ |
| Lysionotus kwangsiensis | PQ468975.1 | 153692 | View on NCBI ↗ |
| Lysionotus levipes | PQ468989.1 | 153644 | View on NCBI ↗ |
| Lysionotus longipedunculatus | PQ468964.1 | 154198 | View on NCBI ↗ |
| Lysionotus metuoensis | PQ468974.1 | 153682 | View on NCBI ↗ |
| Lysionotus microphyllus var. omeiensis | PQ468994.1 | 153796 | View on NCBI ↗ |
| Lysionotus oblongifolius | PQ468965.1 | 154184 | View on NCBI ↗ |
| Lysionotus pauciflorus | NC_034660.1 | 153856 | View on NCBI ↗ |
| Lysionotus pauciflorus var. ikedae | PQ468992.1 | 153873 | View on NCBI ↗ |
| Lysionotus petelotii | PQ468970.1 | 153820 | View on NCBI ↗ |
| Lysionotus pubescens | PQ468973.1 | 153535 | View on NCBI ↗ |
| Lysionotus serratus | PQ468976.1 | 153833 | View on NCBI ↗ |
| Lysionotus sessilifolius | PQ468971.1 | 153912 | View on NCBI ↗ |
| Lysionotus sulphureoides | PQ468972.1 | 153546 | View on NCBI ↗ |
| Lysionotus wilsonii | PQ468969.1 | 153809 | View on NCBI ↗ |