| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16-trnQ-UUG | LSC | 1280 | 0.0150 | 1.00 | 71.6 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 998 | 0.0138 | 0.96 | 72.2 | yes | View details |
| rpoB-trnC-GCA | LSC | 1209 | 0.0130 | 0.99 | 76.5 | yes | View details |
| trnT-GGU-psbD | LSC | 1087 | 0.0104 | 0.99 | 59.3 | yes | View details |
| ndhC-trnV-UAC | LSC | 888 | 0.0137 | 1.00 | 69.4 | yes | View details |
| rbcL-accD | LSC | 699 | 0.0138 | 1.00 | 63.4 | yes | View details |
| accD | LSC | 1479 | 0.0161 | 1.00 | 70.1 | yes | View details |
| ndhF-rpl32 | SSC | 912 | 0.0144 | 0.99 | 67.9 | yes | View details |
| rpl32-trnL-UAG | SSC | 809 | 0.0180 | 1.00 | 74.1 | yes | View details |
| rps15-ycf1 | SSC | 445 | 0.0190 | 1.00 | 63.2 | yes | View details |
| trnK-UUU-rps16 | LSC | 637 | 0.0135 | 0.97 | 79.7 | yes | View details |
| rps19-psbA | LSC | 135 | 0.0580 | 1.00 | 75.5 | no | View details |
| trnC-GCA-petN | LSC | 969 | 0.0114 | 0.98 | 72.1 | yes | View details |
| petN-psbM | LSC | 971 | 0.0088 | 0.99 | 71.5 | yes | View details |
| ccsA-ndhD | SSC | 231 | 0.0255 | 1.00 | 69.5 | yes | View details |
| ycf4-cemA | LSC | 592 | 0.0142 | 0.98 | 67.7 | yes | View details |
| matK-trnK-UUU | LSC | 755 | 0.0076 | 1.00 | 67.2 | yes | View details |
| psbE-petL | LSC | 1019 | 0.0112 | 1.00 | 67.2 | yes | View details |
| psbM-trnD-GUC | LSC | 1091 | 0.0081 | 1.00 | 65.8 | yes | View details |
| psbI-trnS-GCU | LSC | 127 | 0.0414 | 0.95 | 65.3 | 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
39
Genome length
153–155 kb
Candidate markers
271
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 271 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 |
|---|---|---|---|---|---|---|
| trnK-UUU_p1 | trnK-UUU | TTTCAAGGACTCCCAAGCAC |
TCGATCGTATCCGCATATCA |
2830–2928 | 0.846 | 68.4 |
| trnK-UUU_p2 | trnK-UUU | GGACTCCCAAGCACACATAC |
TCGATCGTATCCGCATATCA |
2824–2922 | 0.846 | 66.4 |
| trnK-UUU_p3 | trnK-UUU | TTTCAAGGACTCCCAAGCAC |
TTCGATCGTATCCGCATATCA |
2831–2929 | 0.846 | 66.4 |
| trnK-UUU_p4 | trnK-UUU | CCCACAGGCTTGTACTTTCA |
TCGATCGTATCCGCATATCA |
2896–2994 | 0.846 | 66.2 |
| trnK-UUU_p5 | trnK-UUU | ACGGAAGTGGGTGAAAATAGA |
GACAAATGATGGGTTTGCCG |
2916–2949 | 0.308 | 38.2 |
| matK-trnK-UUU_p1 | matK-trnK-UUU | TAGGAAGTGTTGTTGCCGAG |
TGGGTTGCTAACTCAATGGT |
757–855 | 1.000 | 80.5 |
| matK-trnK-UUU_p2 | matK-trnK-UUU | TAGGAAGTGTTGTTGCCGAG |
TCTGGGTTGCTAACTCAATGG |
759–857 | 1.000 | 79.7 |
| matK-trnK-UUU_p3 | matK-trnK-UUU | TAGGAAGTGTTGTTGCCGAG |
CTGGGTTGCTAACTCAATGGT |
758–856 | 1.000 | 78.6 |
| matK-trnK-UUU_p4 | matK-trnK-UUU | GGAAGTGTTGTTGCCGAGAT |
TGGGTTGCTAACTCAATGGT |
755–853 | 1.000 | 78.0 |
| matK-trnK-UUU_p5 | matK-trnK-UUU | AAGTGTTGTTGCCGAGATCT |
TGGGTTGCTAACTCAATGGT |
753–851 | 0.949 | 75.0 |
| trnK-UUU-rps16_p1 | trnK-UUU-rps16 | AGTCGCACTTAAAAGCCGAA |
GGTGCTCAACCTACAGGAAC |
631–776 | 1.000 | 89.5 |
| trnK-UUU-rps16_p2 | trnK-UUU-rps16 | TAGTCGCACTTAAAAGCCGA |
GGTGCTCAACCTACAGGAAC |
632–777 | 1.000 | 84.6 |
| trnK-UUU-rps16_p3 | trnK-UUU-rps16 | AGTCGCACTTAAAAGCCGAA |
GTGCTCAACCTACAGGAACT |
630–775 | 1.000 | 84.3 |
| trnK-UUU-rps16_p4 | trnK-UUU-rps16 | GTCGCACTTAAAAGCCGAAT |
GGTGCTCAACCTACAGGAAC |
630–775 | 1.000 | 83.3 |
| trnK-UUU-rps16_p5 | trnK-UUU-rps16 | ACCATTGAGTTAGCAACCCA |
GGTGCTCAACCTACAGGAAC |
605–750 | 1.000 | 82.7 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | TATGTCCTTCAAGTCGCACG |
GAGGTTCGAATCCTTCCGTC |
959–1555 | 1.000 | 91.3 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
949–1545 | 1.000 | 90.3 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | TATGTCCTTCAAGTCGCACG |
CTCGGAGGTTCGAATCCTTC |
963–1559 | 1.000 | 90.2 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
CTCGGAGGTTCGAATCCTTC |
953–1549 | 1.000 | 89.2 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | TATGTCCTTCAAGTCGCACG |
TACTCGGAGGTTCGAATCCT |
965–1561 | 1.000 | 88.5 |
| psbI-trnS-GCU_p1 | psbI-trnS-GCU | GATCCGGGCCGTAATCCT |
ATTGGGAGAGATGGCTGAGT |
193–260 | 0.974 | 69.8 |
| psbI-trnS-GCU_p2 | psbI-trnS-GCU | GATCCGGGCCGTAATCCT |
GGGTTCGAATCCCTCTCTCT |
124–191 | 0.974 | 69.0 |
| psbI-trnS-GCU_p3 | psbI-trnS-GCU | GATCCGGGCCGTAATCCT |
GTGGACTAAAGCGGCAGATT |
175–242 | 0.974 | 68.6 |
| psbI-trnS-GCU_p4 | psbI-trnS-GCU | GATCCGGGCCGTAATCCT |
TGGACTAAAGCGGCAGATTG |
174–241 | 0.974 | 68.6 |
| psbI-trnS-GCU_p5 | psbI-trnS-GCU | GATCCGGGCCGTAATCCT |
TTCGAATCCCTCTCTCTCCG |
121–188 | 0.974 | 68.2 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | TCGAACCCTCGGTACAAGTA |
AACCGAAAGACCCCTTAACT |
997–1143 | 1.000 | 77.2 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | GGAACGGAGAGAGAGGGATT |
AACCGAAAGACCCCTTAACT |
1016–1162 | 1.000 | 76.9 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | AATCTGCCGCTTTAGTCCAC |
AACCGAAAGACCCCTTAACT |
958–1104 | 1.000 | 76.8 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | CAATCTGCCGCTTTAGTCCA |
AACCGAAAGACCCCTTAACT |
959–1105 | 1.000 | 76.8 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | CGGAGAGAGAGGGATTCGAA |
AACCGAAAGACCCCTTAACT |
1012–1158 | 1.000 | 76.1 |
Result downloads
Reference species (39)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Muscari adilii | PQ210146.1 | 154021 | View on NCBI ↗ |
| Muscari alpanicum | PQ210178.1 | 153983 | View on NCBI ↗ |
| Muscari anatolicum | PQ210155.1 | 154649 | View on NCBI ↗ |
| Muscari armeniacum | PQ210141.1 | 154402 | View on NCBI ↗ |
| Muscari aucheri | PQ210182.1 | 154512 | View on NCBI ↗ |
| Muscari azureum | PQ210151.1 | 154052 | View on NCBI ↗ |
| Muscari babachii | PQ210162.1 | 154051 | View on NCBI ↗ |
| Muscari botryoides subsp. botryoides | OR896884.1 | 154773 | View on NCBI ↗ |
| Muscari bourgaei | PQ210152.1 | 154228 | View on NCBI ↗ |
| Muscari caucasicum | PQ210161.1 | 154522 | View on NCBI ↗ |
| Muscari coeleste | PQ210147.1 | 154051 | View on NCBI ↗ |
| Muscari commutatum | PQ210133.1 | 154895 | View on NCBI ↗ |
| Muscari comosum | OR896885.1 | 154156 | View on NCBI ↗ |
| Muscari cycladicum | PQ210135.1 | 154168 | View on NCBI ↗ |
| Muscari discolor | PQ210138.1 | 154286 | View on NCBI ↗ |
| Muscari erdalii | PQ210163.1 | 154530 | View on NCBI ↗ |
| Muscari forniculatum | PQ210127.1 | 154193 | View on NCBI ↗ |
| Muscari inconstrictum | PQ210171.1 | 154245 | View on NCBI ↗ |
| Muscari latifolium | PQ210149.1 | 154465 | View on NCBI ↗ |
| Muscari longipes | PQ210157.1 | 154572 | View on NCBI ↗ |
| Muscari macbeathianum | PQ210156.1 | 154636 | View on NCBI ↗ |
| Muscari macrocarpum | PQ210144.1 | 155061 | View on NCBI ↗ |
| Muscari massayanum | PQ210158.1 | 154482 | View on NCBI ↗ |
| Muscari matritense | PQ210186.1 | 154115 | View on NCBI ↗ |
| Muscari microstomum | PQ210154.1 | 154062 | View on NCBI ↗ |
| Muscari mirum | PQ210160.1 | 154143 | View on NCBI ↗ |
| Muscari neglectum | OR896886.1 | 154118 | View on NCBI ↗ |
| Muscari olivetorum | PQ210176.1 | 154115 | View on NCBI ↗ |
| Muscari parviflorum | PQ210164.1 | 154423 | View on NCBI ↗ |
| Muscari pseudomuscari | PQ210194.1 | 154356 | View on NCBI ↗ |
| Muscari racemosum | PQ210143.1 | 154883 | View on NCBI ↗ |
| Muscari sandrasicum | PQ210150.1 | 154912 | View on NCBI ↗ |
| Muscari serpentinicum | PQ210159.1 | 154916 | View on NCBI ↗ |
| Muscari sivrihisardaghlarense | PQ210145.1 | 154048 | View on NCBI ↗ |
| Muscari spreitzenhoferi | PQ210193.1 | 154591 | View on NCBI ↗ |
| Muscari tenuiflorum | PQ210177.1 | 154481 | View on NCBI ↗ |
| Muscari turcicum | PQ210153.1 | 152977 | View on NCBI ↗ |
| Muscari vuralii | PQ210140.1 | 154072 | View on NCBI ↗ |
| Muscari weissii | PQ210136.1 | 154176 | View on NCBI ↗ |