| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| ndhJ-trnF-GAA | LSC | 551 | 0.0238 | 0.99 | 73.5 | yes | View details |
| trnL-UAA-trnQ-UUG | LSC | 658 | 0.0273 | 1.00 | 79.3 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 774 | 0.0220 | 1.00 | 75.1 | yes | View details |
| trnT-UGU-accD | LSC | 1578 | 0.0160 | 0.99 | 67.5 | yes | View details |
| ndhI-ndhF | IRb | 246 | 0.0494 | 0.98 | 77.6 | yes | View details |
| ndhF | SSC | 2235 | 0.0125 | 1.00 | 57.2 | yes | View details |
| rpl32-trnL-UAG | SSC | 774 | 0.0440 | 0.99 | 81.0 | yes | View details |
| ccsA-ndhD | SSC | 327 | 0.0339 | 1.00 | 72.3 | yes | View details |
| ndhG-ndhI | IRa | 303 | 0.0507 | 0.99 | 79.7 | yes | View details |
| atpH-atpI | LSC | 1365 | 0.0174 | 0.99 | 84.5 | yes | View details |
| psaC-ndhE | SSC | 243 | 0.0274 | 1.00 | 76.5 | yes | View details |
| rps19-rpl2 | IRb | 95 | 0.0537 | 1.00 | 75.1 | yes | View details |
| ycf4-cemA | LSC | 626 | 0.0177 | 1.00 | 75.0 | yes | View details |
| rps4-trnT-UGU | LSC | 575 | 0.0159 | 0.99 | 74.9 | yes | View details |
| trnR-UCU-atpA | LSC | 461 | 0.0205 | 1.00 | 74.7 | yes | View details |
| psbI-trnS-GCU | LSC | 170 | 0.0349 | 1.00 | 74.3 | yes | View details |
| atpF-atpH | LSC | 425 | 0.0150 | 1.00 | 73.5 | yes | View details |
| ndhE-ndhG | SSC | 182 | 0.0361 | 1.00 | 72.4 | 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
25
Genome length
164–166 kb
Candidate markers
271
Primer pairs
90
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 271 candidates).
Primer pairs
Showing the top 30 of 90 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| ndhJ-trnF-GAA_p1 | ndhJ-trnF-GAA | TGAAATACAGGATGCTCGTTGA |
GGGATAGCTCAGCTGGTAGA |
637–662 | 0.920 | 71.2 |
| ndhJ-trnF-GAA_p2 | ndhJ-trnF-GAA | TGAAATACAGGATGCTCGTTGA |
CCTCGTGTCACCAGTTCAAA |
601–626 | 0.920 | 70.8 |
| ndhJ-trnF-GAA_p3 | ndhJ-trnF-GAA | TGAAATACAGGATGCTCGTTGA |
CTGGTAGAGCAGAGGACTGA |
625–650 | 0.920 | 70.1 |
| ndhJ-trnF-GAA_p4 | ndhJ-trnF-GAA | TGAAATACAGGATGCTCGTTGA |
AGTTCAAATCTGGTTCCCGG |
589–614 | 0.920 | 69.6 |
| ndhJ-trnF-GAA_p5 | ndhJ-trnF-GAA | TGAAATACAGGATGCTCGTTGA |
ATGGGGATGCATCAGGAATG |
660–685 | 0.920 | 68.7 |
| trnL-UAA-trnQ-UUG_p1 | trnL-UAA-trnQ-UUG | ACCAATTTCGCCATATCCCC |
GGGTTCGAATCCTTCCGTC |
562–921 | 1.000 | 83.5 |
| trnL-UAA-trnQ-UUG_p2 | trnL-UAA-trnQ-UUG | ACCAATTTCGCCATATCCCC |
GGTTCGAATCCTTCCGTCC |
561–777 | 1.000 | 83.5 |
| trnL-UAA-trnQ-UUG_p3 | trnL-UAA-trnQ-UUG | ACCAATTTCGCCATATCCCC |
GTTCGAATCCTTCCGTCCC |
560–776 | 1.000 | 83.5 |
| trnL-UAA-trnQ-UUG_p4 | trnL-UAA-trnQ-UUG | ACCAATTTCGCCATATCCCC |
ACTATATAAATGGGGCGTGGC |
621–980 | 1.000 | 83.1 |
| trnL-UAA-trnQ-UUG_p5 | trnL-UAA-trnQ-UUG | TAGCGTCTACCAATTTCGCC |
GTTCGAATCCTTCCGTCCC |
568–784 | 1.000 | 83.0 |
| psbI-trnS-GCU_p1 | psbI-trnS-GCU | TCTAACGATCCAGGACGAAA |
TAAAGCGCCGGATTGCTAAT |
263–283 | 1.000 | 75.8 |
| psbI-trnS-GCU_p2 | psbI-trnS-GCU | TCTAACGATCCAGGACGAAA |
TAGGGAGAGATGGCTGAGTG |
286–306 | 1.000 | 75.4 |
| psbI-trnS-GCU_p3 | psbI-trnS-GCU | TCTAACGATCCAGGACGAAA |
TTTTTCGTACCGAGGGTTCG |
231–251 | 1.000 | 74.3 |
| psbI-trnS-GCU_p4 | psbI-trnS-GCU | ATCTAACGATCCAGGACGAA |
TAAAGCGCCGGATTGCTAAT |
264–284 | 1.000 | 73.9 |
| psbI-trnS-GCU_p5 | psbI-trnS-GCU | ATCTAACGATCCAGGACGAA |
TAGGGAGAGATGGCTGAGTG |
287–307 | 1.000 | 73.6 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | ATTAGCAATCCGGCGCTTTA |
GGGTCAATAGAACGAATCACAC |
651–884 | 1.000 | 68.8 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
GGGTCAATAGAACGAATCACAC |
700–933 | 1.000 | 67.9 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | GCTTTAGTCCACTCAGCCAT |
GGGTCAATAGAACGAATCACAC |
637–870 | 1.000 | 65.8 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | ATTAGCAATCCGGCGCTTTA |
GGGTCAATAGAACGAATCACA |
651–884 | 1.000 | 65.3 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AGTCCACTCAGCCATCTCTC |
GGGTCAATAGAACGAATCACAC |
632–865 | 1.000 | 65.0 |
| trnR-UCU-atpA_p1 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
CTACCAAGACATTCACCGGG |
428–597 | 1.000 | 78.2 |
| trnR-UCU-atpA_p2 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
TTCAGGAAGAGATGGAACGC |
380–549 | 1.000 | 75.4 |
| trnR-UCU-atpA_p3 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
CAGGAAGAGATGGAACGCTT |
378–547 | 1.000 | 75.3 |
| trnR-UCU-atpA_p4 | trnR-UCU-atpA | TGGATAGGACAGAGGTCTTCT |
CTACCAAGACATTCACCGGG |
463–632 | 1.000 | 75.0 |
| trnR-UCU-atpA_p5 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
TCAGGAAGAGATGGAACGCT |
379–548 | 1.000 | 75.0 |
| atpF-atpH_p1 | atpF-atpH | GTGGCCAATAACCCAAGGAA |
GTTGTGGCATTAGCGCTTTT |
508–522 | 1.000 | 88.6 |
| atpF-atpH_p2 | atpF-atpH | TGGCCAATAACCCAAGGAAA |
GTTGTGGCATTAGCGCTTTT |
507–521 | 1.000 | 83.6 |
| atpF-atpH_p3 | atpF-atpH | GTGGCCAATAACCCAAGGAA |
ATTTATGGGCTGGTTGTGGC |
520–534 | 1.000 | 82.7 |
| atpF-atpH_p4 | atpF-atpH | GTGGCCAATAACCCAAGGAA |
GGAGGCGGAGGGAAAAATAC |
584–598 | 0.920 | 82.6 |
| atpF-atpH_p5 | atpF-atpH | GTGGCCAATAACCCAAGGAA |
GAGGCGGAGGGAAAAATACG |
583–597 | 0.920 | 79.6 |
Result downloads
Reference species (25)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Monnina bonplandiana | PP883909.1 | 165042 | View on NCBI ↗ |
| Monnina carmelensis | PP883912.1 | 165299 | View on NCBI ↗ |
| Monnina cestrifolia | PP883897.1 | 165363 | View on NCBI ↗ |
| Monnina conferta | PP883938.1 | 164359 | View on NCBI ↗ |
| Monnina confusa | PP883948.1 | 164888 | View on NCBI ↗ |
| Monnina crassifolia | PP883907.1 | 165187 | View on NCBI ↗ |
| Monnina denticulata | PP883935.1 | 164871 | View on NCBI ↗ |
| Monnina equatoriensis | PP883906.1 | 165358 | View on NCBI ↗ |
| Monnina fastigiata | PP883911.1 | 165230 | View on NCBI ↗ |
| Monnina fosbergii | PP883951.1 | 165270 | View on NCBI ↗ |
| Monnina herbacea | PP883901.1 | 164436 | View on NCBI ↗ |
| Monnina hirta | PP883919.1 | 165428 | View on NCBI ↗ |
| Monnina hirtella | PP883896.1 | 165441 | View on NCBI ↗ |
| Monnina leptostachya | PP883899.1 | 165012 | View on NCBI ↗ |
| Monnina loxensis | PP883928.1 | 165247 | View on NCBI ↗ |
| Monnina marginata | PP883929.1 | 164867 | View on NCBI ↗ |
| Monnina phillyreoides | PP883905.1 | 164597 | View on NCBI ↗ |
| Monnina pichinchensis | PP883902.1 | 164894 | View on NCBI ↗ |
| Monnina pterocarpa | PP883936.1 | 164851 | View on NCBI ↗ |
| Monnina pycnophylla | PP883947.1 | 165380 | View on NCBI ↗ |
| Monnina salicifolia | PP883937.1 | 164769 | View on NCBI ↗ |
| Monnina sandemanii | PP883927.1 | 165280 | View on NCBI ↗ |
| Monnina sodiroana | PP883903.1 | 165510 | View on NCBI ↗ |
| Monnina splendens | PP883904.1 | 165388 | View on NCBI ↗ |
| Monnina subspeciosa | PP883900.1 | 164734 | View on NCBI ↗ |