| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | Genome | 267 | 0.0202 | 0.99 | 56.1 | yes | View details |
| rps16-trnQ-UUG | Genome | 806 | 0.0110 | 0.99 | 56.7 | yes | View details |
| trnR-UCU-atpA | Genome | 681 | 0.0150 | 0.81 | 63.9 | yes | View details |
| petN-psbM | Genome | 1231 | 0.0085 | 0.98 | 60.4 | yes | View details |
| trnE-UUC-trnT-GGU | Genome | 585 | 0.0111 | 0.91 | 55.4 | yes | View details |
| trnT-GGU-psbD | Genome | 1410 | 0.0045 | 0.99 | 51.5 | yes | View details |
| psbZ-trnG-UCC | Genome | 466 | 0.0159 | 0.96 | 65.8 | yes | View details |
| trnT-UGU-trnL-UAA | Genome | 1263 | 0.0136 | 0.96 | 70.9 | yes | View details |
| ndhC-trnV-UAC | Genome | 588 | 0.0300 | 0.94 | 68.1 | yes | View details |
| accD-psaI | Genome | 792 | 0.0082 | 0.96 | 48.2 | yes | View details |
| petA-psbJ | Genome | 1017 | 0.0070 | 0.97 | 44.9 | yes | View details |
| ndhF-rpl32 | Genome | 1097 | 0.0084 | 0.97 | 65.1 | yes | View details |
| rpl32-trnL-UAG | Genome | 1395 | 0.0077 | 0.99 | 62.0 | yes | View details |
| rps19-trnH-GUG | Genome | 50 | 0.0729 | 0.78 | 60.0 | no | View details |
| psbE-petL | Genome | 1221 | 0.0042 | 1.00 | 59.5 | yes | View details |
| petG-trnW-CCA | Genome | 124 | 0.0267 | 1.00 | 58.1 | yes | View details |
| rpl14-rpl16 | Genome | 152 | 0.0074 | 0.99 | 53.4 | yes | View details |
| psbM-trnD-GUC | Genome | 1238 | 0.0038 | 0.99 | 53.1 | yes | View details |
| trnF-GAA-ndhJ | Genome | 699 | 0.0043 | 1.00 | 51.3 | yes | View details |
| rpoB-trnC-GCA | Genome | 1210 | 0.0021 | 1.00 | 50.8 | yes | View details |
| trnP-UGG-psaJ | Genome | 440 | 0.0054 | 0.96 | 50.8 | 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
159–160 kb
Candidate markers
251
Primer pairs
100
Genome-wide nucleotide diversity
Candidate markers
13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 251 candidates).
Primer pairs
Showing the top 30 of 100 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| trnH-GUG-psbA_p1 | trnH-GUG-psbA | ATATTATGGGCGAACGACGG |
CCTCTAGACCTAGCTGCTGT |
378–403 | 1.000 | 86.9 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
GCGCTAACCTTGGTATGGAA |
367–392 | 1.000 | 86.9 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | ATATTATGGGCGAACGACGG |
GCGCTAACCTTGGTATGGAA |
428–453 | 1.000 | 86.8 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | ATATTATGGGCGAACGACGG |
TTCCCTCTAGACCTAGCTGC |
381–406 | 1.000 | 86.8 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
GCGCTAACCTTGGTATGGAA |
381–406 | 1.000 | 86.7 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
879–909 | 1.000 | 85.0 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | CGTTGCTTTCTTCCACATCG |
GAGGTTCGAATCCTTCCGTC |
860–890 | 1.000 | 84.8 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | CCACAGCTGATCATGTCCTT |
GAGGTTCGAATCCTTCCGTC |
889–919 | 1.000 | 83.3 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | TCCACAGCTGATCATGTCCT |
GAGGTTCGAATCCTTCCGTC |
890–920 | 1.000 | 83.2 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GTGTCGACTAGAAATGGGGC |
941–971 | 1.000 | 82.6 |
| trnR-UCU-atpA_p1 | trnR-UCU-atpA | TGGAATGAAAAGCGTCCATTG |
AGACATTTACCGACGAAGCG |
436–850 | 1.000 | 73.1 |
| trnR-UCU-atpA_p2 | trnR-UCU-atpA | GGAATGAAAAGCGTCCATTGT |
AGACATTTACCGACGAAGCG |
435–849 | 1.000 | 73.1 |
| trnR-UCU-atpA_p3 | trnR-UCU-atpA | GGTTCAAATCCTATTGGACGC |
AGACATTTACCGACGAAGCG |
375–789 | 1.000 | 72.5 |
| trnR-UCU-atpA_p4 | trnR-UCU-atpA | TGGATAGGACAGAGGTCTTCT |
AGACATTTACCGACGAAGCG |
410–824 | 1.000 | 69.4 |
| trnR-UCU-atpA_p5 | trnR-UCU-atpA | TGGAATGAAAAGCGTCCATT |
AGACATTTACCGACGAAGCG |
436–850 | 1.000 | 69.0 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | TAAGCCCTGCTCAATGAACC |
CCGGATTTGAACTGGGGAAA |
1359–1398 | 1.000 | 80.8 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | TAAGCCCTGCTCAATGAACC |
AAAAGGATTTGCAGTCCCCC |
1341–1380 | 1.000 | 78.6 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | TATTGCCTCATTTCCACCCC |
CCGGATTTGAACTGGGGAAA |
1293–1332 | 1.000 | 78.3 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | CTCTGTTAAGCCCTGCTCAA |
CCGGATTTGAACTGGGGAAA |
1365–1404 | 1.000 | 78.0 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | GTTCCTCTGTTAAGCCCTGC |
CCGGATTTGAACTGGGGAAA |
1369–1408 | 1.000 | 77.4 |
| petN-psbM_p1 | petN-psbM | AGTAAATCTCGCTTGGGCTG |
AAAACAGTCAGCCAAGGTGA |
1298–1342 | 1.000 | 83.0 |
| petN-psbM_p2 | petN-psbM | AGTATGGGGAAGGAGTGGAC |
AAAACAGTCAGCCAAGGTGA |
1241–1285 | 1.000 | 82.4 |
| petN-psbM_p3 | petN-psbM | GTATGGGGAAGGAGTGGACT |
AAAACAGTCAGCCAAGGTGA |
1240–1284 | 1.000 | 82.4 |
| petN-psbM_p4 | petN-psbM | TATGGGGAAGGAGTGGACTC |
AAAACAGTCAGCCAAGGTGA |
1239–1283 | 1.000 | 81.9 |
| petN-psbM_p5 | petN-psbM | GGGGAAGGAGTGGACTCTAG |
AAAACAGTCAGCCAAGGTGA |
1236–1280 | 1.000 | 81.6 |
| psbM-trnD-GUC_p1 | psbM-trnD-GUC | TCACCTTGGCTGACTGTTTT |
TTCAATTGGTCAGAGCACCG |
1385–1417 | 1.000 | 75.8 |
| psbM-trnD-GUC_p2 | psbM-trnD-GUC | AATCACCTTGGCTGACTGTT |
TTCAATTGGTCAGAGCACCG |
1387–1419 | 1.000 | 74.0 |
| psbM-trnD-GUC_p3 | psbM-trnD-GUC | ATCACCTTGGCTGACTGTTT |
TTCAATTGGTCAGAGCACCG |
1386–1418 | 1.000 | 74.0 |
| psbM-trnD-GUC_p4 | psbM-trnD-GUC | TCACCTTGGCTGACTGTTTT |
GTTCAATTGGTCAGAGCACC |
1386–1418 | 1.000 | 71.6 |
| psbM-trnD-GUC_p5 | psbM-trnD-GUC | ATCACCTTGGCTGACTGTTTT |
TTCAATTGGTCAGAGCACCG |
1386–1418 | 1.000 | 70.9 |
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 |
|---|---|---|---|
| Crataegus altaica | NC_085640.1 | 159854 | View on NCBI ↗ |
| Crataegus aurantia | NC_085587.1 | 159430 | View on NCBI ↗ |
| Crataegus brachyacantha | PQ283266.1 | 159095 | View on NCBI ↗ |
| Crataegus bretschneideri | OP964009.1 | 159717 | View on NCBI ↗ |
| Crataegus chlorosarca | PX413283.1 | 159782 | View on NCBI ↗ |
| Crataegus chungtienensis | NC_065670.1 | 159847 | View on NCBI ↗ |
| Crataegus crus-galli | PX413284.1 | 159771 | View on NCBI ↗ |
| Crataegus cuneata | NC_058896.1 | 159730 | View on NCBI ↗ |
| Crataegus dahurica | PX413285.1 | 159858 | View on NCBI ↗ |
| Crataegus hupehensis | NC_054155.1 | 159766 | View on NCBI ↗ |
| Crataegus iracunda | OR995415.1 | 159944 | View on NCBI ↗ |
| Crataegus kansuensis | NC_039374.1 | 159865 | View on NCBI ↗ |
| Crataegus laevigata | NC_062347.1 | 159616 | View on NCBI ↗ |
| Crataegus marshallii | MK920293.1 | 159660 | View on NCBI ↗ |
| Crataegus maximowiczii | NC_065485.1 | 159875 | View on NCBI ↗ |
| Crataegus mollis | NC_062346.1 | 159476 | View on NCBI ↗ |
| Crataegus monogyna | NC_066002.1 | 159801 | View on NCBI ↗ |
| Crataegus oresbia | NC_065671.1 | 159851 | View on NCBI ↗ |
| Crataegus phaenopyrum | PX413289.1 | 159973 | View on NCBI ↗ |
| Crataegus pinnatifida | NC_057086.1 | 159898 | View on NCBI ↗ |
| Crataegus pinnatifida f. major | NC_065486.1 | 159656 | View on NCBI ↗ |
| Crataegus rhipidophylla | NC_062345.1 | 159786 | View on NCBI ↗ |
| Crataegus sanguinea | NC_085641.1 | 159713 | View on NCBI ↗ |
| Crataegus scabrifolia | NC_065672.1 | 159742 | View on NCBI ↗ |
| Crataegus shandongensis | PQ283267.1 | 159323 | View on NCBI ↗ |
| Crataegus shensiensis | PX413291.1 | 159807 | View on NCBI ↗ |
| Crataegus songarica | NC_085642.1 | 159881 | View on NCBI ↗ |
| Crataegus viridis | OP964008.1 | 159654 | View on NCBI ↗ |
| Crataegus wilsonii | NC_085643.1 | 159879 | View on NCBI ↗ |
| Crataegus x lavalleei | PX413298.1 | 159771 | View on NCBI ↗ |