| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| EARO_CP_t001-psbA | LSC | 480 | 0.0220 | 0.96 | 71.3 | yes | View details |
| psbZ-EARO_CP_t013 | LSC | 671 | 0.0186 | 1.00 | 77.2 | yes | View details |
| psaA-ycf3 | LSC | 787 | 0.0135 | 0.98 | 71.5 | yes | View details |
| petA-psbJ | LSC | 995 | 0.0122 | 1.00 | 57.6 | yes | View details |
| rps19 | LSC | 279 | 0.0061 | 1.00 | 31.3 | yes | View details |
| ycf1 | SSC | 1101 | 0.0034 | 0.99 | 48.4 | no | View details |
| ndhF | SSC | 2238 | 0.0060 | 1.00 | 49.4 | yes | View details |
| ndhF-rpl32 | SSC | 927 | 0.0125 | 1.00 | 67.2 | yes | View details |
| rpl32-EARO_CP_t030 | SSC | 599 | 0.0249 | 0.99 | 81.4 | yes | View details |
| ycf1 | SSC | 5634 | 0.0114 | 1.00 | 58.6 | yes | View details |
| rps19-rpl2 | IRb | 61 | 0.0850 | 0.89 | 74.5 | yes | View details |
| atpH-atpI | LSC | 1111 | 0.0071 | 1.00 | 74.0 | yes | View details |
| EARO_CP_t016-EARO_CP_t017 | LSC | 1245 | 0.0098 | 0.99 | 73.6 | yes | View details |
| accD-psaI | LSC | 759 | 0.0092 | 1.00 | 70.4 | yes | View details |
| rpl2-EARO_CP_t001 | IRa | 41 | 0.1230 | 0.85 | 68.5 | no | View details |
| rbcL-accD | LSC | 716 | 0.0089 | 0.99 | 67.9 | yes | View details |
| EARO_CP_t004-EARO_CP_t005 | LSC | 787 | 0.0099 | 1.00 | 67.3 | yes | View details |
| EARO_CP_t010-EARO_CP_t011 | LSC | 910 | 0.0086 | 1.00 | 67.3 | yes | View details |
| psbE-petL | LSC | 1283 | 0.0089 | 0.99 | 66.6 | yes | View details |
| ndhC-EARO_CP_t019 | LSC | 514 | 0.0152 | 1.00 | 65.5 | 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
30
Genome length
160–161 kb
Candidate markers
277
Primer pairs
90
Genome-wide nucleotide diversity
Candidate markers
10 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 90 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| EARO_CP_t001-psbA_p1 | EARO_CP_t001-psbA | GATCCACTTGGCTACATCCG |
CCTCTAGACCTAGCTGCTGT |
383–583 | 1.000 | 90.4 |
| EARO_CP_t001-psbA_p2 | EARO_CP_t001-psbA | CAATCCACTGCCTTGATCCA |
CCTCTAGACCTAGCTGCTGT |
397–597 | 1.000 | 90.4 |
| EARO_CP_t001-psbA_p3 | EARO_CP_t001-psbA | AATCCACTGCCTTGATCCAC |
CCTCTAGACCTAGCTGCTGT |
396–596 | 1.000 | 90.4 |
| EARO_CP_t001-psbA_p4 | EARO_CP_t001-psbA | ACAATCCACTGCCTTGATCC |
CCTCTAGACCTAGCTGCTGT |
398–598 | 1.000 | 90.4 |
| EARO_CP_t001-psbA_p5 | EARO_CP_t001-psbA | GATCCACTTGGCTACATCCG |
TTCCCTCTAGACCTAGCTGC |
386–586 | 1.000 | 90.4 |
| EARO_CP_t004-EARO_CP_t005_p1 | EARO_CP_t004-EARO_CP_t005 | CAATCCGACGCTTTAGTCCA |
AAATCAAACCGAGGGATCCC |
893–930 | 1.000 | 83.5 |
| EARO_CP_t004-EARO_CP_t005_p2 | EARO_CP_t004-EARO_CP_t005 | AATCCGACGCTTTAGTCCAC |
AAATCAAACCGAGGGATCCC |
892–929 | 1.000 | 83.5 |
| EARO_CP_t004-EARO_CP_t005_p3 | EARO_CP_t004-EARO_CP_t005 | ACGGAAAGAGAGGGATTCGA |
AAATCAAACCGAGGGATCCC |
947–984 | 1.000 | 82.0 |
| EARO_CP_t004-EARO_CP_t005_p4 | EARO_CP_t004-EARO_CP_t005 | AGCAATCCGACGCTTTAGTC |
AAATCAAACCGAGGGATCCC |
895–932 | 1.000 | 80.7 |
| EARO_CP_t004-EARO_CP_t005_p5 | EARO_CP_t004-EARO_CP_t005 | CGACGCTTTAGTCCACTCAG |
AAATCAAACCGAGGGATCCC |
888–925 | 1.000 | 80.6 |
| atpH-atpI_p1 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TTTTTGCAACTTTAGCCGCG |
1167–1230 | 1.000 | 83.9 |
| atpH-atpI_p2 | atpH-atpI | AATAGAAGCAAGCCCGACAG |
TTTTTGCAACTTTAGCCGCG |
1201–1264 | 1.000 | 83.8 |
| atpH-atpI_p3 | atpH-atpI | AATAGAAGCAAGCCCGACAG |
TAGGTGAATCCATGGAGGGT |
1174–1237 | 1.000 | 83.4 |
| atpH-atpI_p4 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TAGGTGAATCCATGGAGGGT |
1140–1203 | 1.000 | 83.4 |
| atpH-atpI_p5 | atpH-atpI | TACCTTGACCAACTCCAGGT |
TTTTTGCAACTTTAGCCGCG |
1223–1286 | 1.000 | 83.2 |
| EARO_CP_t010-EARO_CP_t011_p1 | EARO_CP_t010-EARO_CP_t011 | TTTCGTAGTACCCTACCCCC |
GAACCGATGACTTACGCCTT |
1019–1061 | 1.000 | 87.4 |
| EARO_CP_t010-EARO_CP_t011_p2 | EARO_CP_t010-EARO_CP_t011 | TTTCGTAGTACCCTACCCCC |
CCATGGCGTTACTCTACCAC |
998–1040 | 1.000 | 87.1 |
| EARO_CP_t010-EARO_CP_t011_p3 | EARO_CP_t010-EARO_CP_t011 | TTTCGTAGTACCCTACCCCC |
TGGCGTTACTCTACCACTGA |
995–1037 | 1.000 | 86.9 |
| EARO_CP_t010-EARO_CP_t011_p4 | EARO_CP_t010-EARO_CP_t011 | GCTGCCTCCTTGAAAGAGAG |
GAACCGATGACTTACGCCTT |
981–1023 | 1.000 | 86.8 |
| EARO_CP_t010-EARO_CP_t011_p5 | EARO_CP_t010-EARO_CP_t011 | TGTCCTGAACCACTAGACGA |
GAACCGATGACTTACGCCTT |
960–1002 | 1.000 | 86.7 |
| psbZ-EARO_CP_t013_p1 | psbZ-EARO_CP_t013 | GACGGTTGGTCGAGTAACAA |
CGTCTTCTCCTTGGCAAAGA |
548–1020 | 1.000 | 88.3 |
| psbZ-EARO_CP_t013_p2 | psbZ-EARO_CP_t013 | ACGGTTGGTCGAGTAACAAA |
CGTCTTCTCCTTGGCAAAGA |
547–1019 | 1.000 | 84.6 |
| psbZ-EARO_CP_t013_p3 | psbZ-EARO_CP_t013 | TTTGCTTCTCCTGACGGTTG |
CGTCTTCTCCTTGGCAAAGA |
560–1012 | 0.967 | 84.0 |
| psbZ-EARO_CP_t013_p4 | psbZ-EARO_CP_t013 | ATTTGCTTCTCCTGACGGTT |
CGTCTTCTCCTTGGCAAAGA |
561–1013 | 0.967 | 82.7 |
| psbZ-EARO_CP_t013_p5 | psbZ-EARO_CP_t013 | GACGGTTGGTCGAGTAACAA |
ACTTTAACCTGGGCGGATAG |
583–1055 | 0.967 | 79.7 |
| psaA-ycf3_p1 | psaA-ycf3 | TGAGAAATGACCCGGTTTGG |
ATCAAGCCGCTGAGTATTGG |
913–999 | 1.000 | 86.9 |
| psaA-ycf3_p2 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
ATCAAGCCGCTGAGTATTGG |
894–980 | 1.000 | 86.8 |
| psaA-ycf3_p3 | psaA-ycf3 | TGAGAAATGACCCGGTTTGG |
AGCGCAGAATTGGTTGAAGA |
855–941 | 1.000 | 86.7 |
| psaA-ycf3_p4 | psaA-ycf3 | GCCCATTCCTCGAAAGAAGT |
AGCGCAGAATTGGTTGAAGA |
836–922 | 1.000 | 86.6 |
| psaA-ycf3_p5 | psaA-ycf3 | TGAGAAATGACCCGGTTTGG |
CGATCAAGCCGCTGAGTATT |
915–1001 | 1.000 | 86.2 |
Result downloads
Reference species (30)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Eucalyptus aromaphloia | NC_022396.1 | 160149 | View on NCBI ↗ |
| Eucalyptus baxteri | NC_022382.1 | 160032 | View on NCBI ↗ |
| Eucalyptus camaldulensis | NC_022398.1 | 160164 | View on NCBI ↗ |
| Eucalyptus cladocalyx | NC_022394.1 | 160213 | View on NCBI ↗ |
| Eucalyptus cloeziana | NC_022388.1 | 160015 | View on NCBI ↗ |
| Eucalyptus curtisii | NC_022391.1 | 160038 | View on NCBI ↗ |
| Eucalyptus deglupta | NC_022399.1 | 160177 | View on NCBI ↗ |
| Eucalyptus delegatensis | NC_022380.1 | 159724 | View on NCBI ↗ |
| Eucalyptus diversicolor | NC_022402.1 | 160214 | View on NCBI ↗ |
| Eucalyptus diversifolia | NC_022383.1 | 159954 | View on NCBI ↗ |
| Eucalyptus elata | NC_022385.1 | 159899 | View on NCBI ↗ |
| Eucalyptus erythrocorys | NC_022406.1 | 159742 | View on NCBI ↗ |
| Eucalyptus globulus subsp. globulus | NC_008115.1 | 160286 | View on NCBI ↗ |
| Eucalyptus guilfoylei | NC_022405.1 | 160520 | View on NCBI ↗ |
| Eucalyptus marginata | NC_022390.1 | 160076 | View on NCBI ↗ |
| Eucalyptus melliodora | NC_022392.1 | 160386 | View on NCBI ↗ |
| Eucalyptus microcorys | NC_022404.1 | 160225 | View on NCBI ↗ |
| Eucalyptus nitens | NC_022395.1 | 160271 | View on NCBI ↗ |
| Eucalyptus obliqua | NC_022378.1 | 159527 | View on NCBI ↗ |
| Eucalyptus patens | NC_022389.1 | 160187 | View on NCBI ↗ |
| Eucalyptus polybractea | NC_022393.1 | 160268 | View on NCBI ↗ |
| Eucalyptus radiata | NC_022379.1 | 159529 | View on NCBI ↗ |
| Eucalyptus regnans | NC_022386.1 | 160031 | View on NCBI ↗ |
| Eucalyptus robusta | MZ670598.1 | 160201 | View on NCBI ↗ |
| Eucalyptus saligna | NC_022397.1 | 160015 | View on NCBI ↗ |
| Eucalyptus salmonophloia | NC_022403.1 | 160413 | View on NCBI ↗ |
| Eucalyptus sieberi | NC_022384.1 | 159985 | View on NCBI ↗ |
| Eucalyptus torquata | NC_022401.1 | 160223 | View on NCBI ↗ |
| Eucalyptus umbra | NC_022387.1 | 159576 | View on NCBI ↗ |
| Eucalyptus verrucata | NC_022381.1 | 160109 | View on NCBI ↗ |