| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| trnH-GUG-psbA | LSC | 369 | 0.0061 | 1.00 | 55.8 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 1086 | 0.0027 | 1.00 | 59.0 | yes | View details |
| rpoB-trnC-GCA | LSC | 4263 | 0.0014 | 1.00 | 48.1 | yes | View details |
| trnC-GCA-petN | LSC | 883 | 0.0084 | 1.00 | 62.5 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 976 | 0.0050 | 0.97 | 61.4 | yes | View details |
| psbB-psbT | LSC | 160 | 0.0006 | 1.00 | 29.0 | yes | View details |
| rps11 | LSC | 417 | 0.0025 | 1.00 | 35.0 | yes | View details |
| rpl16 | LSC | 1383 | 0.0023 | 1.00 | 52.3 | yes | View details |
| trnR-ACG-trnN-GUU | IRb | 611 | 0.0034 | 1.00 | 51.4 | yes | View details |
| ndhF | SSC | 2244 | 0.0020 | 1.00 | 43.3 | yes | View details |
| ndhF-rpl32 | SSC | 983 | 0.0037 | 1.00 | 57.3 | yes | View details |
| rpl32-trnL-UAG | SSC | 624 | 0.0025 | 1.00 | 56.1 | yes | View details |
| ndhA | SSC | 2264 | 0.0020 | 1.00 | 52.6 | yes | View details |
| trnT-GGU-psbD | LSC | 1394 | 0.0023 | 1.00 | 64.6 | yes | View details |
| trnF-GAA-ndhJ | LSC | 748 | 0.0027 | 1.00 | 56.2 | yes | View details |
| psbT-psbN | LSC | 71 | 0.0241 | 1.00 | 56.1 | yes | View details |
| psaJ-rpl33 | LSC | 513 | 0.0039 | 0.99 | 53.9 | yes | View details |
| pafI-trnS-GGA | LSC | 918 | 0.0025 | 0.99 | 53.3 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 974 | 0.0031 | 1.00 | 53.0 | yes | View details |
| trnK-UUU-rps16 | LSC | 975 | 0.0017 | 1.00 | 52.6 | yes | View details |
| psbE-petL | LSC | 1166 | 0.0008 | 1.00 | 52.5 | yes | View details |
| clpP | LSC | 2406 | 0.0010 | 1.00 | 52.5 | 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
21
Genome length
161–163 kb
Candidate markers
268
Primer pairs
115
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 268 candidates).
Primer pairs
Showing the top 30 of 115 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 |
430–447 | 1.000 | 84.2 |
| trnH-GUG-psbA_p2 | trnH-GUG-psbA | GATCCACTTGGCTACATCCG |
GCGCTAACCTTGGTATGGAA |
477–494 | 1.000 | 84.0 |
| trnH-GUG-psbA_p3 | trnH-GUG-psbA | CAATCCACTGCCTTGATCCA |
GCGCTAACCTTGGTATGGAA |
491–508 | 1.000 | 83.8 |
| trnH-GUG-psbA_p4 | trnH-GUG-psbA | AATCCACTGCCTTGATCCAC |
GCGCTAACCTTGGTATGGAA |
490–507 | 1.000 | 83.8 |
| trnH-GUG-psbA_p5 | trnH-GUG-psbA | ACAATCCACTGCCTTGATCC |
GCGCTAACCTTGGTATGGAA |
492–509 | 1.000 | 83.8 |
| trnK-UUU_p1 | trnK-UUU | TGATACGCACATGACTTCGA |
TGTCCTACATACAAAACACAGGT |
2954–2970 | 0.905 | 43.3 |
| trnK-UUU_p2 | trnK-UUU | GTGATACGCACATGACTTCG |
TGTCCTACATACAAAACACAGGT |
2955–2971 | 0.905 | 43.0 |
| trnK-UUU_p3 | trnK-UUU | TGATACGCACATGACTTCGA |
TTCAAGTGTCAATGGATCCA |
2992–2998 | 0.857 | 39.8 |
| trnK-UUU_p4 | trnK-UUU | GTGATACGCACATGACTTCG |
TTCAAGTGTCAATGGATCCA |
2993–2999 | 0.857 | 39.4 |
| trnK-UUU_p5 | trnK-UUU | TGATACGCACATGACTTCGA |
TCAAGTGTCAATGGATCCAT |
2991–2997 | 0.857 | 37.8 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | CGAATCCCTTGCTTCATCCA |
ATTTTCTTGAAAGGGGCGCT |
1130–1175 | 1.000 | 80.2 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | ACGAATCCCTTGCTTCATCC |
ATTTTCTTGAAAGGGGCGCT |
1131–1176 | 1.000 | 80.2 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | GGACGAATCCCTTGCTTCAT |
ATTTTCTTGAAAGGGGCGCT |
1133–1178 | 1.000 | 80.2 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | AACTCTACCGATGGTGTGGA |
ATTTTCTTGAAAGGGGCGCT |
1150–1195 | 1.000 | 80.0 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | GACCCTAGCCGCACTTAAAA |
ATTTTCTTGAAAGGGGCGCT |
1099–1144 | 1.000 | 79.8 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
ACGAATCACACTTTTACCACT |
1192–1247 | 1.000 | 55.9 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | CGAATGACTCGTACAACGGA |
ACGAATCACACTTTTACCACT |
1162–1217 | 1.000 | 55.2 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
GAACGAATCACACTTTTACCACT |
1194–1249 | 1.000 | 54.8 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | ACGGAAAGAGAGGGATTCGA |
AGGAATCAAATTGAAGGATCCCT |
1228–1269 | 0.952 | 53.9 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | CGAATGACTCGTACAACGGA |
AGGAATCAAATTGAAGGATCCCT |
1198–1239 | 0.952 | 53.3 |
| rpoB-trnC-GCA_p1 | rpoB-trnC-GCA | GCGGGGGTCTATCCAAATTT |
TCCCTAATGACATAAGAAAGTCAA |
304–332 | 1.000 | 44.9 |
| rpoB-trnC-GCA_p2 | rpoB-trnC-GCA | GCGGGGGTCTATCCAAATTT |
TCCCTAATGACATAAGAAAGTCAAA |
304–332 | 1.000 | 44.9 |
| rpoB-trnC-GCA_p3 | rpoB-trnC-GCA | GCGGGGGTCTATCCAAATTT |
TGTTTCCCTAATGACATAAGAAAGT |
308–336 | 1.000 | 44.8 |
| rpoB-trnC-GCA_p4 | rpoB-trnC-GCA | GCGGGGGTCTATCCAAATTT |
TGTTTCCCTAATGACATAAGAAAGTC |
308–336 | 1.000 | 44.8 |
| rpoB-trnC-GCA_p5 | rpoB-trnC-GCA | GCGGGGGTCTATCCAAATTT |
TTCCCTAATGACATAAGAAAGTCAA |
305–333 | 1.000 | 44.8 |
| trnC-GCA-petN_p1 | trnC-GCA-petN | TTTCCCCGGTTCAAATCTGG |
CCATACGACGAGTGAAAGGG |
953–1000 | 1.000 | 88.5 |
| trnC-GCA-petN_p2 | trnC-GCA-petN | TTTCCCCGGTTCAAATCTGG |
CCCATACGACGAGTGAAAGG |
954–1001 | 1.000 | 88.4 |
| trnC-GCA-petN_p3 | trnC-GCA-petN | TTTCCCCGGTTCAAATCTGG |
CCCCATACGACGAGTGAAAG |
955–1002 | 1.000 | 88.4 |
| trnC-GCA-petN_p4 | trnC-GCA-petN | TTTCCCCGGTTCAAATCTGG |
AGCCCAAGCGAGACTTACTA |
908–955 | 1.000 | 88.2 |
| trnC-GCA-petN_p5 | trnC-GCA-petN | TTTCCCCGGTTCAAATCTGG |
AGTCCACTTCTCCCCCATAC |
967–1014 | 1.000 | 88.0 |
Result downloads
Reference species (21)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Calligonum aphyllum | NC_049137.1 | 161251 | View on NCBI ↗ |
| Calligonum bakuense | NC_062619.1 | 162129 | View on NCBI ↗ |
| Calligonum caput-medusae | NC_049141.1 | 162019 | View on NCBI ↗ |
| Calligonum colubrinum | NC_049142.1 | 161321 | View on NCBI ↗ |
| Calligonum cordatum | NC_049143.1 | 161276 | View on NCBI ↗ |
| Calligonum densum | NC_049144.1 | 161264 | View on NCBI ↗ |
| Calligonum ebinuricum | NC_049145.1 | 161265 | View on NCBI ↗ |
| Calligonum gobicum | NC_049139.1 | 161375 | View on NCBI ↗ |
| Calligonum jeminaicum | NC_049146.1 | 162535 | View on NCBI ↗ |
| Calligonum junceum | NC_049147.1 | 162036 | View on NCBI ↗ |
| Calligonum juochiangense | NC_049138.1 | 161355 | View on NCBI ↗ |
| Calligonum klementzii | NC_049148.1 | 161405 | View on NCBI ↗ |
| Calligonum korlaense | NC_049149.1 | 161339 | View on NCBI ↗ |
| Calligonum leucocladum | NC_053260.1 | 161279 | View on NCBI ↗ |
| Calligonum mongolicum | NC_053261.1 | 161316 | View on NCBI ↗ |
| Calligonum pumilum | NC_053262.1 | 161324 | View on NCBI ↗ |
| Calligonum roborowskii | NC_053263.1 | 161367 | View on NCBI ↗ |
| Calligonum rubicundum | NC_053264.1 | 161184 | View on NCBI ↗ |
| Calligonum squarrosum | NC_053265.1 | 161320 | View on NCBI ↗ |
| Calligonum taklimakanense | NC_053266.1 | 161629 | View on NCBI ↗ |
| Calligonum yengisaricum | NC_053267.1 | 161391 | View on NCBI ↗ |