| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnS-GCU-trnG-UCC | LSC | 880 | 0.0146 | 0.97 | 75.9 | yes | View details |
| atpF | LSC | 1420 | 0.0092 | 0.97 | 62.1 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 967 | 0.0110 | 0.93 | 67.0 | yes | View details |
| ndhC-trnV-UAC | LSC | 1726 | 0.0110 | 0.98 | 68.1 | yes | View details |
| rbcL | LSC | 1464 | 0.0090 | 1.00 | 51.1 | yes | View details |
| accD | LSC | 1476 | 0.0148 | 1.00 | 57.6 | yes | View details |
| ndhF-rpl32 | SSC | 1025 | 0.0117 | 0.96 | 62.6 | yes | View details |
| rpl32-trnL-UAG | SSC | 808 | 0.0126 | 0.99 | 67.5 | yes | View details |
| ndhD | SSC | 1506 | 0.0046 | 1.00 | 46.0 | yes | View details |
| ycf1 | SSC | 5424 | 0.0084 | 1.00 | 53.2 | yes | View details |
| psaA-ycf3 | LSC | 640 | 0.0083 | 1.00 | 65.7 | yes | View details |
| atpH-atpI | LSC | 497 | 0.0065 | 0.98 | 60.9 | yes | View details |
| psbM-trnD-GUC | LSC | 1070 | 0.0067 | 0.99 | 60.6 | yes | View details |
| rpoB-trnC-GCA | LSC | 1229 | 0.0074 | 0.99 | 60.5 | yes | View details |
| petA-psbJ | LSC | 1001 | 0.0078 | 0.99 | 60.2 | yes | View details |
| clpP | LSC | 2094 | 0.0048 | 0.99 | 59.9 | yes | View details |
| trnT-GGU-psbD | LSC | 1046 | 0.0048 | 1.00 | 59.7 | yes | View details |
| ndhG-ndhI | SSC | 348 | 0.0192 | 0.99 | 58.6 | yes | View details |
| ycf4-cemA | LSC | 548 | 0.0050 | 0.99 | 58.2 | yes | View details |
| trnL-UAA-trnF-GAA | LSC | 349 | 0.0113 | 1.00 | 58.1 | 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
156–157 kb
Candidate markers
277
Primer pairs
100
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 100 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | AATCAGAGGAAGCGGAGAGA |
ACGAATCGCACTTTTACCACT |
999–1119 | 1.000 | 79.2 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | AATCAGAGGAAGCGGAGAGA |
ACGAATCGCACTTTTACCAC |
999–1119 | 1.000 | 79.2 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | AATCTGCCGCTTTAGTCCAC |
ACGAATCGCACTTTTACCACT |
933–1053 | 1.000 | 78.7 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | CAATCTGCCGCTTTAGTCCA |
ACGAATCGCACTTTTACCACT |
934–1054 | 1.000 | 78.7 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | AATCTGCCGCTTTAGTCCAC |
ACGAATCGCACTTTTACCAC |
933–1053 | 1.000 | 78.6 |
| atpF_p1 | atpF | CGAAGAGTTACCATTAGCGTCT |
AGAACTCTGTTCTTTGTTAGTCCT |
1527–1569 | 1.000 | 48.1 |
| atpF_p2 | atpF | CGAAGAGTTACCATTAGCGTCT |
AGAACGACTCAAGTGATACA |
1550–1592 | 1.000 | 48.0 |
| atpF_p3 | atpF | CGAAGAGTTACCATTAGCGTCT |
AAGAACGACTCAAGTGATACA |
1551–1593 | 1.000 | 48.0 |
| atpF_p4 | atpF | CGAAGAGTTACCATTAGCGTCT |
AGAACGACTCAAGTGATACAA |
1550–1592 | 1.000 | 48.0 |
| atpF_p5 | atpF | CGAAGAGTTACCATTAGCGTCT |
AGAACGACTCAAGTGATACAAA |
1550–1592 | 1.000 | 48.0 |
| atpH-atpI_p1 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TAGGGGAATCAATGGAGGGT |
546–565 | 1.000 | 81.2 |
| atpH-atpI_p2 | atpH-atpI | CGCAATACCTTCTACGGCTT |
TAGGGGAATCAATGGAGGGT |
634–653 | 1.000 | 80.3 |
| atpH-atpI_p3 | atpH-atpI | ATAACGGAAGCGGCAGAAAT |
TTTTTGCAACTTTAGCCGCG |
573–592 | 0.971 | 80.3 |
| atpH-atpI_p4 | atpH-atpI | CGCAATACCTTCTACGGCTT |
TTTTTGCAACTTTAGCCGCG |
661–680 | 0.971 | 79.5 |
| atpH-atpI_p5 | atpH-atpI | TACCTTGACCAACTCCAGGT |
TTTTTGCAACTTTAGCCGCG |
629–648 | 0.971 | 79.2 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | AAATTCTTCTGCCAAGCCCT |
ATCTTTTGTTGCTCAGGCGA |
1413–1463 | 1.000 | 82.8 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | CTTCTGCCAAGCCCTGATTA |
ATCTTTTGTTGCTCAGGCGA |
1408–1458 | 1.000 | 81.9 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | AATTCTTCTGCCAAGCCCTG |
ATCTTTTGTTGCTCAGGCGA |
1412–1462 | 1.000 | 81.7 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | TCCCTCATTTCCATTCCGGA |
ATCTTTTGTTGCTCAGGCGA |
1332–1382 | 0.943 | 79.9 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | TTCCCTCATTTCCATTCCGG |
ATCTTTTGTTGCTCAGGCGA |
1333–1383 | 0.943 | 79.7 |
| psbM-trnD-GUC_p1 | psbM-trnD-GUC | ATGAACAGCGCAGTAGCAAT |
TTCAATTGGTCAGAGCACCG |
1157–1196 | 1.000 | 80.4 |
| psbM-trnD-GUC_p2 | psbM-trnD-GUC | TGAACAGCGCAGTAGCAATA |
TTCAATTGGTCAGAGCACCG |
1156–1195 | 1.000 | 79.4 |
| psbM-trnD-GUC_p3 | psbM-trnD-GUC | ACAGCGCAGTAGCAATAAGT |
TTCAATTGGTCAGAGCACCG |
1153–1192 | 1.000 | 79.4 |
| psbM-trnD-GUC_p4 | psbM-trnD-GUC | ATGAACAGCGCAGTAGCAAT |
TGCTATACACCTCACTGGGA |
1183–1222 | 0.914 | 76.2 |
| psbM-trnD-GUC_p5 | psbM-trnD-GUC | TGAACAGCGCAGTAGCAATA |
TGCTATACACCTCACTGGGA |
1182–1221 | 0.914 | 75.2 |
| trnT-GGU-psbD_p1 | trnT-GGU-psbD | GTGGTAGAGTAACGCCATGG |
GGACCACCCTACAAAAACGA |
1186–1236 | 1.000 | 84.0 |
| trnT-GGU-psbD_p2 | trnT-GGU-psbD | TCAGTGGTAGAGTAACGCCA |
GGACCACCCTACAAAAACGA |
1189–1239 | 0.971 | 82.5 |
| trnT-GGU-psbD_p3 | trnT-GGU-psbD | GGCGTAAGTCATCGGTTCAA |
GGACCACCCTACAAAAACGA |
1163–1213 | 1.000 | 82.2 |
| trnT-GGU-psbD_p4 | trnT-GGU-psbD | GGCCCTTTTAACTCAGTGGT |
GGACCACCCTACAAAAACGA |
1201–1251 | 1.000 | 82.2 |
| trnT-GGU-psbD_p5 | trnT-GGU-psbD | TGGTAGAGTAACGCCATGGT |
GGACCACCCTACAAAAACGA |
1185–1235 | 1.000 | 81.0 |
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 |
|---|---|---|---|
| Asparagus alopecurus | OR571500.1 | 156710 | View on NCBI ↗ |
| Asparagus angulofractus | OQ851310.1 | 156744 | View on NCBI ↗ |
| Asparagus brachyphyllus | OQ851320.1 | 156779 | View on NCBI ↗ |
| Asparagus breslerianus | OR571495.1 | 156735 | View on NCBI ↗ |
| Asparagus cf. pseudoscaber PB-2023 | OR571512.1 | 156813 | View on NCBI ↗ |
| Asparagus cochinchinensis | PV276193.1 | 156389 | View on NCBI ↗ |
| Asparagus cooperi | OR571506.1 | 157164 | View on NCBI ↗ |
| Asparagus dauricus | OQ851329.1 | 156766 | View on NCBI ↗ |
| Asparagus densiflorus | PV658263.1 | 157116 | View on NCBI ↗ |
| Asparagus exuvialis | OR571494.1 | 156920 | View on NCBI ↗ |
| Asparagus falcatus | NC_086746.1 | 157128 | View on NCBI ↗ |
| Asparagus flagellaris | OR571493.1 | 156808 | View on NCBI ↗ |
| Asparagus gobicus | OQ851318.1 | 156757 | View on NCBI ↗ |
| Asparagus kiusianus | OR571488.1 | 156765 | View on NCBI ↗ |
| Asparagus laricinus | OR571508.1 | 156980 | View on NCBI ↗ |
| Asparagus longiflorus | OQ851312.1 | 156735 | View on NCBI ↗ |
| Asparagus lycopodineus | NC_085423.1 | 156805 | View on NCBI ↗ |
| Asparagus macowanii | OQ851347.1 | 156968 | View on NCBI ↗ |
| Asparagus meioclados | NC_080871.1 | 156515 | View on NCBI ↗ |
| Asparagus munitus | NC_080870.1 | 156381 | View on NCBI ↗ |
| Asparagus myriacanthus | OR187836.1 | 156939 | View on NCBI ↗ |
| Asparagus neglectus | OQ851311.1 | 156787 | View on NCBI ↗ |
| Asparagus nelsii | PV087174.1 | 157048 | View on NCBI ↗ |
| Asparagus officinalis | NC_034777.1 | 156699 | View on NCBI ↗ |
| Asparagus officinalis subsp. officinalis | OR896873.1 | 156740 | View on NCBI ↗ |
| Asparagus oligoclonos | OQ851315.1 | 156735 | View on NCBI ↗ |
| Asparagus petersianus | OR571491.1 | 156930 | View on NCBI ↗ |
| Asparagus retrofractus | OR571501.1 | 156990 | View on NCBI ↗ |
| Asparagus schoberioides | NC_035969.1 | 156875 | View on NCBI ↗ |
| Asparagus setaceus | NC_047458.1 | 156978 | View on NCBI ↗ |
| Asparagus subscandens | NC_086747.1 | 156985 | View on NCBI ↗ |
| Asparagus taliensis | NC_088049.1 | 155940 | View on NCBI ↗ |
| Asparagus tibeticus | OQ851321.1 | 156683 | View on NCBI ↗ |
| Asparagus trichoclados | OQ851314.1 | 156828 | View on NCBI ↗ |
| Asparagus virgatus | OQ851332.1 | 157064 | View on NCBI ↗ |