| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnR-UCU-trnG-UCC | LSC | 235 | 0.0161 | 0.98 | 59.0 | yes | View details |
| trnG-UCC-trnT-GGU | LSC | 418 | 0.0341 | 0.83 | 70.3 | yes | View details |
| trnT-GGU-psbD | LSC | 1333 | 0.0080 | 0.99 | 64.6 | yes | View details |
| psbZ-trnG-UCC | LSC | 312 | 0.0095 | 1.00 | 41.3 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 557 | 0.0133 | 0.99 | 66.8 | yes | View details |
| ndhC-trnV-UAC | LSC | 711 | 0.0095 | 0.99 | 73.5 | yes | View details |
| accD-psaI | LSC | 886 | 0.0127 | 0.95 | 59.6 | yes | View details |
| rpl16-rps3 | LSC | 1165 | 0.0071 | 0.99 | 55.2 | yes | View details |
| ycf1-rps15 | SSC | 403 | 0.0098 | 1.00 | 46.0 | yes | View details |
| ndhD | SSC | 1503 | 0.0028 | 1.00 | 40.9 | yes | View details |
| trnL-UAG-rpl32 | SSC | 711 | 0.0102 | 1.00 | 61.8 | yes | View details |
| rpl32-ndhF | SSC | 1045 | 0.0093 | 0.98 | 53.9 | yes | View details |
| ndhF | SSC | 2226 | 0.0041 | 1.00 | 41.0 | yes | View details |
| atpA-trnR-UCU | LSC | 135 | 0.0283 | 0.99 | 69.7 | yes | View details |
| rpl22-rps19 | LSC | 80 | 0.0310 | 0.96 | 69.7 | yes | View details |
| psbI-trnS-GCU | LSC | 147 | 0.0186 | 1.00 | 64.6 | yes | View details |
| trnY-GUA-rpoB | LSC | 1222 | 0.0063 | 0.99 | 60.3 | yes | View details |
| psaC-ndhD | SSC | 112 | 0.0321 | 0.98 | 59.2 | yes | View details |
| ndhF-ycf1 | SSC | 50 | 0.0843 | 0.48 | 58.0 | yes | View details |
| ycf4-cemA | LSC | 873 | 0.0062 | 0.99 | 57.8 | yes | View details |
| rpoC2-rps2 | LSC | 230 | 0.0110 | 1.00 | 57.3 | yes | View details |
| petA-psbJ | LSC | 714 | 0.0062 | 1.00 | 56.5 | 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
151–153 kb
Candidate markers
268
Primer pairs
110
Genome-wide nucleotide diversity
Candidate markers
13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).
Primer pairs
Showing the top 30 of 110 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| psbI-trnS-GCU_p1 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGA |
ATTGGGAGAGATGGCTGAGT |
257–283 | 1.000 | 77.7 |
| psbI-trnS-GCU_p2 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGA |
CGAGTTATTCGTACCGAGGG |
205–231 | 1.000 | 76.9 |
| psbI-trnS-GCU_p3 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGAA |
ATTGGGAGAGATGGCTGAGT |
257–283 | 1.000 | 75.4 |
| psbI-trnS-GCU_p4 | psbI-trnS-GCU | CCTATCCAATGATCCAGGACG |
ATTGGGAGAGATGGCTGAGT |
276–302 | 1.000 | 74.2 |
| psbI-trnS-GCU_p5 | psbI-trnS-GCU | CGTAATCCTGGACGTGAAGA |
GATGGCTGAGTGGACGAAAG |
248–274 | 1.000 | 73.7 |
| trnY-GUA-rpoB_p1 | trnY-GUA-rpoB | CAACGAATTTACAGTCCGCC |
AGTTCTTCTGTCAAACCCTGA |
1336–1387 | 0.963 | 62.5 |
| trnY-GUA-rpoB_p2 | trnY-GUA-rpoB | AACGAATTTACAGTCCGCCC |
AGTTCTTCTGTCAAACCCTGA |
1335–1386 | 0.963 | 62.3 |
| trnY-GUA-rpoB_p3 | trnY-GUA-rpoB | AGATTGGCAAATTGTTGGGC |
TCAAACCCTGATCAATGAACCT |
1379–1430 | 0.963 | 61.4 |
| trnY-GUA-rpoB_p4 | trnY-GUA-rpoB | AGATTGGCAAATTGTTGGGC |
AGTTCTTCTGTCAAACCCTGA |
1389–1440 | 0.926 | 60.8 |
| trnY-GUA-rpoB_p5 | trnY-GUA-rpoB | GATTGGCAAATTGTTGGGCC |
AGTTCTTCTGTCAAACCCTGA |
1388–1439 | 0.926 | 60.2 |
| rpoC2-rps2_p1 | rpoC2-rps2 | TGCCTTTCAAAGAATTTCCATGA |
CCATGGCCAAAATGAACTCC |
343–350 | 1.000 | 48.5 |
| rpoC2-rps2_p2 | rpoC2-rps2 | TGCCTTTCAAAGAATTTCCATGA |
GGCCAAAATGAACTCCTGCT |
339–346 | 1.000 | 48.1 |
| rpoC2-rps2_p3 | rpoC2-rps2 | TCTTGCCTTTCAAAGAATTTCCA |
CCATGGCCAAAATGAACTCC |
346–353 | 1.000 | 48.0 |
| rpoC2-rps2_p4 | rpoC2-rps2 | TCTTGCCTTTCAAAGAATTTCCA |
GGCCAAAATGAACTCCTGCT |
342–349 | 1.000 | 47.6 |
| rpoC2-rps2_p5 | rpoC2-rps2 | TGCCTTTCAAAGAATTTCCATGA |
TGGCCAAAATGAACTCCTGC |
340–347 | 1.000 | 45.7 |
| atpA-trnR-UCU_p1 | atpA-trnR-UCU | TACTTCAGGAACAAGCAGCC |
GCAATGAAAAGCGTCCATTGT |
234–249 | 1.000 | 75.3 |
| atpA-trnR-UCU_p2 | atpA-trnR-UCU | TTTACCGAGGAAGCAGAAGC |
GCAATGAAAAGCGTCCATTGT |
295–310 | 1.000 | 74.6 |
| atpA-trnR-UCU_p3 | atpA-trnR-UCU | TACTTCAGGAACAAGCAGCC |
GCAATGAAAAGCGTCCATTG |
234–249 | 1.000 | 74.5 |
| atpA-trnR-UCU_p4 | atpA-trnR-UCU | CAGGAACAGAGGGAACGTTT |
GCAATGAAAAGCGTCCATTGT |
256–271 | 1.000 | 74.1 |
| atpA-trnR-UCU_p5 | atpA-trnR-UCU | TTTACCGAGGAAGCAGAAGC |
GCAATGAAAAGCGTCCATTG |
295–310 | 1.000 | 73.7 |
| trnR-UCU-trnG-UCC_p1 | trnR-UCU-trnG-UCC | AGAAGACCTCTGTCCTATCCA |
AGCCTTCCAAGCTAACGATG |
303–322 | 1.000 | 72.2 |
| trnR-UCU-trnG-UCC_p2 | trnR-UCU-trnG-UCC | AGAAGACCTCTGTCCTATCCA |
CCTAGCCTTCCAAGCTAACG |
306–325 | 1.000 | 72.0 |
| trnR-UCU-trnG-UCC_p3 | trnR-UCU-trnG-UCC | AGGTTTAGAAGACCTCTGTCCT |
AGCCTTCCAAGCTAACGATG |
309–328 | 1.000 | 71.5 |
| trnR-UCU-trnG-UCC_p4 | trnR-UCU-trnG-UCC | AGGTTTAGAAGACCTCTGTCCT |
CCTAGCCTTCCAAGCTAACG |
312–331 | 1.000 | 71.2 |
| trnR-UCU-trnG-UCC_p5 | trnR-UCU-trnG-UCC | AGAAGACCTCTGTCCTATCCA |
CCCTAGCCTTCCAAGCTAAC |
307–326 | 1.000 | 69.7 |
| trnG-UCC-trnT-GGU_p1 | trnG-UCC-trnT-GGU | AATGAAACCGAAAGACCCCT |
TCCCCTATCGGATCTGAACC |
368–561 | 0.889 | 79.7 |
| trnG-UCC-trnT-GGU_p2 | trnG-UCC-trnT-GGU | ATGAAACCGAAAGACCCCTT |
TCCCCTATCGGATCTGAACC |
367–560 | 0.889 | 79.7 |
| trnG-UCC-trnT-GGU_p3 | trnG-UCC-trnT-GGU | GAATGAAACCGAAAGACCCCT |
TCCCCTATCGGATCTGAACC |
369–562 | 0.889 | 77.8 |
| trnG-UCC-trnT-GGU_p4 | trnG-UCC-trnT-GGU | AATGAAACCGAAAGACCCCT |
GATCTGAACCGAGGGCTTAC |
358–551 | 0.852 | 76.5 |
| trnG-UCC-trnT-GGU_p5 | trnG-UCC-trnT-GGU | ATGAAACCGAAAGACCCCTT |
GATCTGAACCGAGGGCTTAC |
357–550 | 0.852 | 76.5 |
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 |
|---|---|---|---|
| Diplostephium azureum | NC_034882.1 | 152124 | View on NCBI ↗ |
| Diplostephium barclayanum | NC_034853.1 | 151974 | View on NCBI ↗ |
| Diplostephium cajamarquillense | NC_034872.1 | 152070 | View on NCBI ↗ |
| Diplostephium callilepis | NC_034856.1 | 152110 | View on NCBI ↗ |
| Diplostephium cinereum | NC_034869.1 | 152554 | View on NCBI ↗ |
| Diplostephium crypteriophyllum | NC_034881.1 | 151665 | View on NCBI ↗ |
| Diplostephium empetrifolium | NC_034891.1 | 152461 | View on NCBI ↗ |
| Diplostephium ericoides | NC_034870.1 | 151982 | View on NCBI ↗ |
| Diplostephium espinosae | NC_034880.1 | 152091 | View on NCBI ↗ |
| Diplostephium foliosissimum | NC_034883.1 | 152260 | View on NCBI ↗ |
| Diplostephium glandulosum | NC_034854.1 | 151400 | View on NCBI ↗ |
| Diplostephium gnidioides | NC_034867.1 | 152144 | View on NCBI ↗ |
| Diplostephium goodspeedii | NC_034901.1 | 152006 | View on NCBI ↗ |
| Diplostephium gynoxyoides | NC_034862.1 | 151662 | View on NCBI ↗ |
| Diplostephium haenkei | NC_034871.1 | 152292 | View on NCBI ↗ |
| Diplostephium hartwegii | NC_034832.1 | 151994 | View on NCBI ↗ |
| Diplostephium hippophae | NC_034831.1 | 152197 | View on NCBI ↗ |
| Diplostephium jelskii | NC_034811.1 | 152142 | View on NCBI ↗ |
| Diplostephium juniperinum | NC_034813.1 | 152454 | View on NCBI ↗ |
| Diplostephium lechleri | NC_034816.1 | 152067 | View on NCBI ↗ |
| Diplostephium meyenii | NC_034824.1 | 152537 | View on NCBI ↗ |
| Diplostephium oblanceolatum | NC_034830.1 | 151895 | View on NCBI ↗ |
| Diplostephium oxapampanum | NC_034815.1 | 151637 | View on NCBI ↗ |
| Diplostephium pulchrum | NC_034810.1 | 152236 | View on NCBI ↗ |
| Diplostephium sagasteguii | NC_034828.1 | 152214 | View on NCBI ↗ |
| Diplostephium serratifolium | NC_034826.1 | 152060 | View on NCBI ↗ |
| Diplostephium spinulosum | NC_034823.1 | 152155 | View on NCBI ↗ |