Markers + reference

Chamaesium

9 species · Apiaceae · Apiales

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Species 9
Genome length 145–156 kb
Candidate markers 273
Primer pairs 100

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 339 0.0866 1.00 77.0 yes View details
trnK-UUU-rps16 LSC 876 0.0290 0.98 73.7 yes View details
rps16-trnQ-UUG LSC 1002 0.0320 1.00 75.8 yes View details
trnS-GCU-trnG-UCC LSC 629 0.0387 1.00 81.6 yes View details
atpF-atpH LSC 365 0.0548 0.97 81.5 yes View details
trnE-UUC-trnT-GGU LSC 705 0.0453 1.00 82.8 yes View details
atpB-rbcL LSC 766 0.0290 1.00 75.3 yes View details
ycf1 IRb 1845 0.0088 1.00 57.4 no View details
ndhF SSC 2217 0.0162 1.00 57.8 yes View details
rpl32-trnL-UAG SSC 782 0.0536 0.98 83.3 yes View details
ycf1 SSC 5175 0.0201 1.00 58.4 yes View details
psaA-ycf3 LSC 707 0.0302 0.98 77.9 yes View details
rpl22-rps19 LSC 70 0.0478 1.00 77.0 yes View details
trnT-UGU-trnL-UAA LSC 779 0.0304 0.97 76.3 yes View details
ccsA-ndhD SSC 226 0.0517 1.00 75.3 yes View details
trnG-UCC-trnR-UCU LSC 260 0.0502 0.86 74.3 yes View details
trnD-GUC-trnY-GUA LSC 109 0.0428 1.00 74.3 yes View details
atpH-atpI LSC 1139 0.0269 0.99 74.2 yes View details
trnM-CAU-atpE LSC 213 0.0408 1.00 74.1 yes View details
psbM-trnD-GUC LSC 547 0.0289 1.00 74.0 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.

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 GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 305–431 0.778 81.6
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 308–434 0.778 81.5
trnH-GUG-psbA_p3 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC CCTCTAGACCTAGCTGCTGT 310–436 0.778 77.7
trnH-GUG-psbA_p4 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC TTCCCTCTAGACCTAGCTGC 313–439 0.778 77.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCCTCTAGACCTAGCTGCTG 306–432 0.778 76.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG TGCTGCCATTTTGGAAGGAT 1389–1647 0.889 85.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAAGAACAGAGGCTCGTTGC GATTCAAAGTGTATCGCGCG 1936–1982 0.889 84.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG GATTCAAAGTGTATCGCGCG 1673–1719 0.778 79.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 TAAGAACAGAGGCTCGTTGC CGATTCAAAGTGTATCGCGC 1937–1983 0.778 78.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG CGATTCAAAGTGTATCGCGC 1674–1720 0.667 74.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGCGCGATACACTTTGAATC CCCGCCCAATCAAAAATTCC 1595–2042 0.889 85.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCTTCCAAAATGGCAGCA CCCGCCCAATCAAAAATTCC 1667–2128 0.889 85.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGCGCGATACACTTTGAATC CGAAAACTTACCGCAGCTTG 1881–2334 0.889 84.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCGCGATACACTTTGAATCG CCCGCCCAATCAAAAATTCC 1594–2041 0.778 79.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCGCGATACACTTTGAATCG CGAAAACTTACCGCAGCTTG 1880–2333 0.778 79.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TACCACTAAACTATACCCGC 672–800 1.000 56.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TACCACTAAACTATACCCGC 667–795 1.000 55.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TTACCACTAAACTATACCCGC 673–801 1.000 55.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TTACCACTAAACTATACCCGC 668–796 1.000 54.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TTTACCACTAAACTATACCCGC 674–802 1.000 53.5
trnG-UCC_p1 trnG-UCC ATTAGCAATCCGCCGCTTTA GAGGAAGCAGAAGCCCTTTT 1908–2047 1.000 90.7
trnG-UCC_p2 trnG-UCC ACTCAGCCATCTCTCCCAAT GAGGAAGCAGAAGCCCTTTT 1884–2023 1.000 90.2
trnG-UCC_p3 trnG-UCC CAAATTCCCCCTGTTCGACA GAGGAAGCAGAAGCCCTTTT 1292–1340 0.889 84.9
trnG-UCC_p4 trnG-UCC TTCCCCCTGTTCGACAAAAG GAGGAAGCAGAAGCCCTTTT 1288–1336 0.778 79.5
trnG-UCC_p5 trnG-UCC GTTCGACAAAAGGCCCTTTG GAGGAAGCAGAAGCCCTTTT 1280–1328 0.778 78.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG GAGGAAGCAGAAGCCCTTTT 506–562 1.000 91.1
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG GGGATCCGCAGCTCAAATTA 855–911 1.000 90.6
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG GGGATCCGCAGCTCAAATTA 858–914 1.000 90.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU AGCTCGGTGGAAACAAAACT GAGGAAGCAGAAGCCCTTTT 811–868 1.000 90.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU AGCTCGGTGGAAACAAAACT GGGATCCGCAGCTCAAATTA 1160–1217 1.000 89.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Chamaesium delavayi PQ551033.1 153991 View on NCBI ↗
Chamaesium jiulongense MN119368.1 154254 View on NCBI ↗
Chamaesium mallaeanum MN119369.2 155712 View on NCBI ↗
Chamaesium novem-jugum MN119370.2 154034 View on NCBI ↗
Chamaesium paradoxum MK780227.1 144558 View on NCBI ↗
Chamaesium spatuliferum MN119371.1 153770 View on NCBI ↗
Chamaesium thalictrifolium MN119372.1 152703 View on NCBI ↗
Chamaesium viridiflorum MN119373.1 154237 View on NCBI ↗
Chamaesium wolffianum MN119374.2 155053 View on NCBI ↗