| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 261 | 0.0124 | 1.00 | 56.9 | yes | View details |
| rps16-trnQ-UUG | LSC | 812 | 0.0072 | 1.00 | 65.0 | yes | View details |
| trnR-UCU-atpA | LSC | 789 | 0.0292 | 0.98 | 70.3 | yes | View details |
| petN-psbM | LSC | 1249 | 0.0063 | 1.00 | 59.2 | yes | View details |
| trnT-GGU-psbD | LSC | 1501 | 0.0101 | 0.98 | 68.5 | yes | View details |
| psbZ-trnG-GCC | LSC | 506 | 0.0145 | 0.92 | 64.4 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 1178 | 0.0065 | 0.99 | 61.3 | yes | View details |
| ndhC-trnV-UAC | LSC | 692 | 0.0161 | 0.94 | 73.0 | yes | View details |
| ndhF-rpl32 | SSC | 1044 | 0.0075 | 1.00 | 53.7 | yes | View details |
| rps19-trnH-GUG | LSC | 38 | 0.0477 | 0.87 | 66.1 | no | View details |
| atpH-atpI | LSC | 1177 | 0.0047 | 1.00 | 63.7 | yes | View details |
| rpl32-trnL | SSC | 1391 | 0.0047 | 1.00 | 58.3 | yes | View details |
| psaA-ycf3 | LSC | 703 | 0.0018 | 0.99 | 53.8 | yes | View details |
| petA-psbJ | LSC | 996 | 0.0050 | 1.00 | 53.7 | yes | View details |
| atpA-atpF | LSC | 54 | 0.0059 | 1.00 | 53.2 | yes | View details |
| psbE-petL | LSC | 1237 | 0.0023 | 1.00 | 53.0 | yes | View details |
| rpl33-rps18 | LSC | 218 | 0.0064 | 1.00 | 52.6 | yes | View details |
| rpoB-trnC-GCA | LSC | 1232 | 0.0035 | 0.98 | 52.4 | yes | View details |
| psbM-trnD-GUC | LSC | 1221 | 0.0035 | 1.00 | 51.7 | 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
43
Genome length
159–160 kb
Candidate markers
270
Primer pairs
90
Genome-wide nucleotide diversity
Candidate markers
9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 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 |
|---|---|---|---|---|---|---|
| trnH-GUG-psbA_p1 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
GCGCTAACCTTGGTATGGAA |
384–431 | 1.000 | 86.4 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
GCGCTAACCTTGGTATGGAA |
383–430 | 1.000 | 86.4 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | ATATTATGGGCGAACGACGG |
CCTCTAGACCTAGCTGCTGT |
381–428 | 0.953 | 83.8 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ATATTATGGGCGAACGACGG |
TTCCCTCTAGACCTAGCTGC |
384–431 | 0.953 | 83.7 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | ATATTATGGGCGAACGACGG |
GCGCTAACCTTGGTATGGAA |
431–478 | 0.953 | 83.3 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
872–902 | 1.000 | 84.9 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | CCACAGCTGATCATGTCCTT |
GAGGTTCGAATCCTTCCGTC |
882–912 | 1.000 | 83.2 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | GCTTTCTGCCACATCGTTTT |
GAGGTTCGAATCCTTCCGTC |
849–879 | 1.000 | 83.2 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | TCCACAGCTGATCATGTCCT |
GAGGTTCGAATCCTTCCGTC |
883–913 | 1.000 | 83.1 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GTGTCGACTAGAAATGGGGC |
934–964 | 1.000 | 82.5 |
| trnR-UCU-atpA_p1 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
AGACATTTACCGACGAAGCG |
376–962 | 1.000 | 75.5 |
| trnR-UCU-atpA_p2 | trnR-UCU-atpA | TGGATAGGACAGAGGTCTTCT |
AGACATTTACCGACGAAGCG |
411–997 | 1.000 | 72.6 |
| trnR-UCU-atpA_p3 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
GGAAGCCCTTTTGAAAGAAGC |
357–943 | 1.000 | 70.2 |
| trnR-UCU-atpA_p4 | trnR-UCU-atpA | GTTCAAATCCTATTGGACGCA |
AGACATTTACCGACGAAGCG |
375–961 | 1.000 | 69.8 |
| trnR-UCU-atpA_p5 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
ACCAAGACATTTACCGACGA |
380–966 | 1.000 | 69.6 |
| atpA-atpF_p1 | atpA-atpF | ATGCCATCGCCTACTTGAAG |
TGGTATGTTTGGAACGGTGA |
205–209 | 1.000 | 74.9 |
| atpA-atpF_p2 | atpA-atpF | GCTCAATACGTTCGCGGATA |
TGGTATGTTTGGAACGGTGA |
144–148 | 1.000 | 74.5 |
| atpA-atpF_p3 | atpA-atpF | ATGCCATCGCCTACTTGAAG |
TGGTATGTTTGGAACGGTGAA |
205–209 | 1.000 | 72.7 |
| atpA-atpF_p4 | atpA-atpF | ATGCCATCGCCTACTTGAAG |
TTGGTATGTTTGGAACGGTGA |
206–210 | 1.000 | 72.7 |
| atpA-atpF_p5 | atpA-atpF | CAATGCCATCGCCTACTTGA |
TGGTATGTTTGGAACGGTGA |
207–211 | 1.000 | 72.6 |
| atpH-atpI_p1 | atpH-atpI | AATAGAAGCAAGCCCGACAG |
GCGAATCCATGGAAGGTCAT |
1236–1270 | 1.000 | 85.8 |
| atpH-atpI_p2 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
GCGAATCCATGGAAGGTCAT |
1202–1236 | 1.000 | 85.8 |
| atpH-atpI_p3 | atpH-atpI | AATAGAAGCAAGCCCGACAG |
TTTTTGCAACCTTAGCTGCG |
1266–1300 | 1.000 | 84.9 |
| atpH-atpI_p4 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TTTTTGCAACCTTAGCTGCG |
1232–1266 | 1.000 | 84.9 |
| atpH-atpI_p5 | atpH-atpI | AATAACGGAAGCGGCAGAAA |
GCGAATCCATGGAAGGTCAT |
1203–1237 | 1.000 | 84.7 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | TAAGCCCTGCTCAATGAACC |
CCGGATTTGAACTGGGGAAA |
1362–1404 | 1.000 | 82.4 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | TAAGCCCTGCTCAATGAACC |
AAAAGGATTTGCAGTCCCCC |
1344–1386 | 1.000 | 80.3 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | TATTGCCTCATTTCCACCCC |
CCGGATTTGAACTGGGGAAA |
1296–1338 | 1.000 | 80.0 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | CTCTGTTAAGCCCTGCTCAA |
CCGGATTTGAACTGGGGAAA |
1368–1410 | 1.000 | 79.6 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | GTTCCTCTGTTAAGCCCTGC |
CCGGATTTGAACTGGGGAAA |
1372–1414 | 1.000 | 79.1 |
Result downloads
Reference species (43)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Malus angustifolia | NC_045410.1 | 160090 | View on NCBI ↗ |
| Malus asiatica | PP595841.1 | 160201 | View on NCBI ↗ |
| Malus baccata var. gracilis | OQ737737.1 | 159992 | View on NCBI ↗ |
| Malus baccata var. xiaojinensis | NC_062348.1 | 160063 | View on NCBI ↗ |
| Malus coronaria | NC_045308.1 | 160295 | View on NCBI ↗ |
| Malus daochengensis | PQ432182.1 | 160019 | View on NCBI ↗ |
| Malus delavayi | NC_045424.1 | 159786 | View on NCBI ↗ |
| Malus doumeri | NC_045343.1 | 159654 | View on NCBI ↗ |
| Malus floribunda | NC_070406.1 | 160037 | View on NCBI ↗ |
| Malus fusca | NC_062349.1 | 159962 | View on NCBI ↗ |
| Malus halliana | NC_085498.1 | 160201 | View on NCBI ↗ |
| Malus honanensis | NC_085523.1 | 159944 | View on NCBI ↗ |
| Malus hupehensis | NC_040170.1 | 160065 | View on NCBI ↗ |
| Malus indica | NC_085588.1 | 159677 | View on NCBI ↗ |
| Malus ioensis | NC_045393.1 | 159841 | View on NCBI ↗ |
| Malus komarovii | PQ432196.1 | 160096 | View on NCBI ↗ |
| Malus leiocalyca | NC_085578.1 | 159429 | View on NCBI ↗ |
| Malus mandshurica | NC_085522.1 | 160067 | View on NCBI ↗ |
| Malus melliana | MW115597.1 | 160175 | View on NCBI ↗ |
| Malus muliensis | NC_085579.1 | 159430 | View on NCBI ↗ |
| Malus niedzwetzkyana | NC_088533.1 | 160230 | View on NCBI ↗ |
| Malus ombrophila | PQ432198.1 | 159925 | View on NCBI ↗ |
| Malus orientalis | NC_062350.1 | 159966 | View on NCBI ↗ |
| Malus orthocarpa | NC_085580.1 | 159989 | View on NCBI ↗ |
| Malus prattii | NC_043902.1 | 160239 | View on NCBI ↗ |
| Malus rockii | NC_062334.1 | 160117 | View on NCBI ↗ |
| Malus sargentii | NC_085521.1 | 159716 | View on NCBI ↗ |
| Malus sieboldii | NC_050059.1 | 160040 | View on NCBI ↗ |
| Malus sieversii | NC_045390.1 | 159895 | View on NCBI ↗ |
| Malus sikkimensis | NC_062333.1 | 160088 | View on NCBI ↗ |
| Malus sylvestris | NC_062299.1 | 159969 | View on NCBI ↗ |
| Malus toringoides | NC_049113.1 | 160093 | View on NCBI ↗ |
| Malus transitoria | PQ432210.1 | 160100 | View on NCBI ↗ |
| Malus trilobata | NC_035671.1 | 160207 | View on NCBI ↗ |
| Malus x atrosanguinea | NC_045409.1 | 160107 | View on NCBI ↗ |
| Malus x dawsoniana | NC_085577.1 | 159990 | View on NCBI ↗ |
| Malus x magdeburgensis | NC_085589.1 | 160233 | View on NCBI ↗ |
| Malus x moerlandsii | MW115610.1 | 160230 | View on NCBI ↗ |
| Malus x platycarpa | NC_085581.1 | 159176 | View on NCBI ↗ |
| Malus x purpurea | NC_085582.1 | 160206 | View on NCBI ↗ |
| Malus x robusta | NC_085499.1 | 160241 | View on NCBI ↗ |
| Malus yunnanensis | NC_039624.1 | 160067 | View on NCBI ↗ |
| Malus zhaojiaoensis | NC_070438.1 | 159998 | View on NCBI ↗ |