| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH_gug-psbA | LSC | 432 | 0.0108 | 0.98 | 52.4 | yes | View details |
| trnR_ucu-atpA | LSC | 253 | 0.0178 | 0.91 | 47.2 | yes | View details |
| petN-psbM | LSC | 1280 | 0.0093 | 0.99 | 56.8 | yes | View details |
| psbM-trnD_guc | LSC | 1204 | 0.0076 | 0.99 | 56.1 | yes | View details |
| ndhJ | LSC | 477 | 0.0032 | 1.00 | 43.9 | yes | View details |
| petA-psbJ | LSC | 1097 | 0.0073 | 0.99 | 57.1 | yes | View details |
| rpl22 | LSC | 492 | 0.0154 | 0.99 | 47.8 | yes | View details |
| ycf1 | IRb | 1092 | 0.0017 | 1.00 | 31.7 | no | View details |
| ndhF-rpl32 | SSC | 1025 | 0.0093 | 1.00 | 54.0 | yes | View details |
| rpl32-trnL_uag | SSC | 1114 | 0.0130 | 0.99 | 56.8 | yes | View details |
| ccsA-ndhD | SSC | 338 | 0.0202 | 0.93 | 48.0 | yes | View details |
| ycf1 | SSC | 5493 | 0.0066 | 1.00 | 48.9 | yes | View details |
| rpl22 | IRa | 242 | 0.0029 | 1.00 | 32.0 | no | View details |
| ndhK-ndhC | LSC | 64 | 0.0146 | 1.00 | 60.1 | yes | View details |
| rpl22-trnH_gug | LSC | 30 | 0.1755 | 0.37 | 60.0 | no | View details |
| ndhE-ndhG | SSC | 277 | 0.0183 | 1.00 | 59.9 | yes | View details |
| rpl14-rpl16 | LSC | 146 | 0.0177 | 0.92 | 58.9 | yes | View details |
| trnT_ugu-trnL_uaa | LSC | 1060 | 0.0080 | 1.00 | 57.6 | yes | View details |
| trnG_gcc-trnfM_cau | LSC | 187 | 0.0121 | 0.99 | 57.1 | yes | View details |
| accD-psaI | LSC | 769 | 0.0077 | 0.99 | 56.6 | yes | View details |
| petL-petG | LSC | 194 | 0.0178 | 0.99 | 56.3 | yes | View details |
| rps16-trnQ_uug | LSC | 1292 | 0.0073 | 1.00 | 55.9 | 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
35
Genome length
160–161 kb
Candidate markers
276
Primer pairs
95
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 276 candidates).
Primer pairs
Showing the top 30 of 95 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 |
TTCCCTCTAGACCTAGCTGC |
438–519 | 0.943 | 85.7 |
| trnH_gug-psbA_p2 | trnH_gug-psbA | CAATCCACTGCCTTGATCCA |
TTCCCTCTAGACCTAGCTGC |
452–533 | 0.943 | 85.5 |
| trnH_gug-psbA_p3 | trnH_gug-psbA | AATCCACTGCCTTGATCCAC |
TTCCCTCTAGACCTAGCTGC |
451–532 | 0.943 | 85.5 |
| trnH_gug-psbA_p4 | trnH_gug-psbA | ACAATCCACTGCCTTGATCC |
TTCCCTCTAGACCTAGCTGC |
453–534 | 0.943 | 85.5 |
| trnH_gug-psbA_p5 | trnH_gug-psbA | CGCATGGTGGATTCACAATC |
TTCCCTCTAGACCTAGCTGC |
467–548 | 0.943 | 82.7 |
| rps16-trnQ_uug_p1 | rps16-trnQ_uug | CAGCGGATCATGTCCTTCAA |
GAGGTTCGAATCCTTCCGTC |
878–1428 | 1.000 | 86.6 |
| rps16-trnQ_uug_p2 | rps16-trnQ_uug | GCGGATCATGTCCTTCAAGT |
GAGGTTCGAATCCTTCCGTC |
876–1426 | 1.000 | 86.6 |
| rps16-trnQ_uug_p3 | rps16-trnQ_uug | CAGCGGATCATGTCCTTCAA |
CGAAATTGAAATGGGGCGTC |
937–1487 | 1.000 | 86.4 |
| rps16-trnQ_uug_p4 | rps16-trnQ_uug | CAGCGGATCATGTCCTTCAA |
GAAATTGAAATGGGGCGTCG |
936–1486 | 1.000 | 86.4 |
| rps16-trnQ_uug_p5 | rps16-trnQ_uug | GCGGATCATGTCCTTCAAGT |
GAAATTGAAATGGGGCGTCG |
934–1484 | 1.000 | 86.4 |
| trnR_ucu-atpA_p1 | trnR_ucu-atpA | AGCCTTCCAAGCTAACGATG |
CTCTCACGGTGGAAGAACAG |
769–806 | 1.000 | 86.6 |
| trnR_ucu-atpA_p2 | trnR_ucu-atpA | AGCCTTCCAAGCTAACGATG |
CGAAGCTTATCCCGGAGATG |
1200–1237 | 1.000 | 84.4 |
| trnR_ucu-atpA_p3 | trnR_ucu-atpA | AGCCTTCCAAGCTAACGATG |
ATCCCTCCAAACAAGCACAG |
1264–1301 | 1.000 | 84.0 |
| trnR_ucu-atpA_p4 | trnR_ucu-atpA | AGCCTTCCAAGCTAACGATG |
GATCCCTCCAAACAAGCACA |
1265–1302 | 1.000 | 84.0 |
| trnR_ucu-atpA_p5 | trnR_ucu-atpA | AGCCTTCCAAGCTAACGATG |
TGATCCCTCCAAACAAGCAC |
1266–1303 | 1.000 | 83.9 |
| petN-psbM_p1 | petN-psbM | TAGTAAGTCTCGCTTGGGCT |
CGTTCTAGTTCCTACTGCGT |
1199–1515 | 1.000 | 79.3 |
| petN-psbM_p2 | petN-psbM | TAGTAAGTCTCGCTTGGGCT |
AGTTCCTACTGCGTTTTTGC |
1193–1509 | 1.000 | 78.1 |
| petN-psbM_p3 | petN-psbM | TAGTAAGTCTCGCTTGGGCT |
GTTCCTACTGCGTTTTTGCT |
1192–1508 | 1.000 | 78.1 |
| petN-psbM_p4 | petN-psbM | ATGGGGAAGAAGTGGACTCT |
CGTTCTAGTTCCTACTGCGT |
1138–1454 | 1.000 | 77.7 |
| petN-psbM_p5 | petN-psbM | TAGTAAGTCTCGCTTGGGCT |
TCGTTCTAGTTCCTACTGCG |
1200–1516 | 1.000 | 77.0 |
| psbM-trnD_guc_p1 | psbM-trnD_guc | ACGCAGTAGGAACTAGAACG |
TTCAATTGGTCAGAGCACCG |
1299–1361 | 1.000 | 74.4 |
| psbM-trnD_guc_p2 | psbM-trnD_guc | AGCAAAAACGCAGTAGGAAC |
TTCAATTGGTCAGAGCACCG |
1306–1368 | 1.000 | 73.3 |
| psbM-trnD_guc_p3 | psbM-trnD_guc | GCAAAAACGCAGTAGGAACT |
TTCAATTGGTCAGAGCACCG |
1305–1367 | 1.000 | 73.3 |
| psbM-trnD_guc_p4 | psbM-trnD_guc | CGCAGTAGGAACTAGAACGA |
TTCAATTGGTCAGAGCACCG |
1298–1360 | 1.000 | 72.2 |
| psbM-trnD_guc_p5 | psbM-trnD_guc | AACGCAGTAGGAACTAGAACG |
TTCAATTGGTCAGAGCACCG |
1300–1362 | 1.000 | 72.1 |
| trnG_gcc-trnfM_cau_p1 | trnG_gcc-trnfM_cau | TCTTTGCCAAGGAGAAGACG |
CTTGAGGTCACGGGTTCAAA |
215–316 | 1.000 | 85.9 |
| trnG_gcc-trnfM_cau_p2 | trnG_gcc-trnfM_cau | TCTTTGCCAAGGAGAAGACG |
GGGTAGAGCAGTTTGGTAGC |
251–352 | 1.000 | 85.6 |
| trnG_gcc-trnfM_cau_p3 | trnG_gcc-trnfM_cau | TCTTTGCCAAGGAGAAGACG |
CCAGTCCTTCTCTTCATCGC |
272–373 | 1.000 | 85.0 |
| trnG_gcc-trnfM_cau_p4 | trnG_gcc-trnfM_cau | TCTTTGCCAAGGAGAAGACG |
TGAGGTCACGGGTTCAAATC |
213–314 | 1.000 | 84.8 |
| trnG_gcc-trnfM_cau_p5 | trnG_gcc-trnfM_cau | TCTTTGCCAAGGAGAAGACG |
TAGCTCGCAAGGCTCATAAC |
235–336 | 1.000 | 84.2 |
Result downloads
Reference species (35)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Citrus australasica | NC_058999.1 | 160335 | View on NCBI ↗ |
| Citrus australis | NC_065752.1 | 160413 | View on NCBI ↗ |
| Citrus benikoji | NC_079953.1 | 160699 | View on NCBI ↗ |
| Citrus cavaleriei | NC_053572.1 | 160996 | View on NCBI ↗ |
| Citrus depressa | NC_031894.1 | 160120 | View on NCBI ↗ |
| Citrus erythrosa | MW722946.1 | 160120 | View on NCBI ↗ |
| Citrus glauca | LC794891.1 | 160450 | View on NCBI ↗ |
| Citrus hindsii | NC_053690.1 | 160145 | View on NCBI ↗ |
| Citrus indica | NC_065753.1 | 160312 | View on NCBI ↗ |
| Citrus jambhiri | NC_065754.1 | 160210 | View on NCBI ↗ |
| Citrus japonica | NC_053733.1 | 160229 | View on NCBI ↗ |
| Citrus japonica var. margarita | NC_072621.1 | 160230 | View on NCBI ↗ |
| Citrus junos | NC_064135.1 | 160612 | View on NCBI ↗ |
| Citrus keraji | NC_064136.1 | 160121 | View on NCBI ↗ |
| Citrus latipes | LC794892.1 | 160145 | View on NCBI ↗ |
| Citrus limonia | NC_065755.1 | 160723 | View on NCBI ↗ |
| Citrus madurensis | NC_064137.1 | 160229 | View on NCBI ↗ |
| Citrus mangshanensis | NC_064138.1 | 160262 | View on NCBI ↗ |
| Citrus maxima | NC_034290.1 | 160133 | View on NCBI ↗ |
| Citrus micrantha | NC_065667.1 | 159928 | View on NCBI ↗ |
| Citrus natsudaidai | NC_079954.1 | 160185 | View on NCBI ↗ |
| Citrus nobilis | NC_065756.1 | 160700 | View on NCBI ↗ |
| Citrus oto | NC_064139.1 | 160127 | View on NCBI ↗ |
| Citrus platymamma | NC_030194.1 | 160121 | View on NCBI ↗ |
| Citrus reticulata | NC_034671.1 | 160100 | View on NCBI ↗ |
| Citrus sinensis | NC_008334.1 | 160129 | View on NCBI ↗ |
| Citrus tachibana | NC_064140.1 | 160600 | View on NCBI ↗ |
| Citrus tangerina | NC_065757.1 | 160699 | View on NCBI ↗ |
| Citrus tarogayo | NC_064141.1 | 160121 | View on NCBI ↗ |
| Citrus unshiu x Citrus sinensis | NC_079821.1 | 160699 | View on NCBI ↗ |
| (Citrus unshiu x Citrus sinensis) x Citrus reticulata | NC_079822.1 | 160699 | View on NCBI ↗ |
| Citrus x clementina | NC_059803.1 | 160702 | View on NCBI ↗ |
| Citrus x latifolia | NC_079825.1 | 160141 | View on NCBI ↗ |
| Citrus x paradisi | NC_063672.1 | 160186 | View on NCBI ↗ |
| Citrus x tangelo | NC_079952.1 | 160183 | View on NCBI ↗ |