Markers + reference

Machilus

22 species · Lauraceae · Laurales

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Species 22
Genome length 153–153 kb
Candidate markers 258
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 396 0.0078 0.95 55.7 yes View details
ycf3-trnS-GGA LSC 812 0.0033 0.99 48.4 yes View details
petA-psbJ LSC 1146 0.0072 1.00 50.7 yes View details
ycf1 IRb 1374 0.0002 1.00 28.9 no View details
ndhF-rpl32 SSC 1229 0.0034 0.92 55.7 yes View details
rpl32-trnL-UAG SSC 1386 0.0034 0.99 58.5 yes View details
ccsA SSC 951 0.0008 1.00 32.2 yes View details
ndhA SSC 2215 0.0017 1.00 47.2 yes View details
ycf1 SSC 5565 0.0014 1.00 45.6 yes View details
clpP LSC 2048 0.0015 1.00 56.4 yes View details
rpl2-rpl23 LSC 29 0.0139 1.00 53.7 yes View details
trnE-UUC-trnT-GGU LSC 724 0.0010 1.00 48.9 yes View details
atpF LSC 1281 0.0005 1.00 48.8 yes View details
trnF-GAA-ndhJ LSC 554 0.0009 1.00 48.4 yes View details
trnK-UUU-rps16 LSC 821 0.0015 1.00 48.3 yes View details
psbM-trnD-GUC LSC 993 0.0012 1.00 48.3 yes View details
rps16-trnQ-UUG LSC 1872 0.0012 0.99 48.1 yes View details
accD-psaI LSC 585 0.0022 1.00 47.3 yes View details
atpA-atpF LSC 70 0.0030 1.00 47.1 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.

Primer pairs

Showing the top 30 of 90 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 444–467 1.000 84.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 458–481 1.000 84.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 457–480 1.000 84.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 459–482 1.000 84.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 473–496 1.000 81.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 949–955 1.000 79.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 948–954 1.000 79.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAAGACCATAGCCGCACTT AAAAAGGCGCTCAACCTACA 970–976 1.000 79.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 958–964 1.000 78.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 952–958 1.000 77.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1931–1946 1.000 79.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGGTACAAGAATCCACAGCC GAGGTTCGAATCCTTCCGTC 1964–1979 1.000 78.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1935–1950 1.000 78.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCCGATAATGTCCTT GAGGTTCGAATCCTTCCGTC 1952–1967 1.000 77.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTACAAGAATCCACAGCCGA GAGGTTCGAATCCTTCCGTC 1962–1977 1.000 77.5
atpA-atpF_p1 atpA-atpF GCCTACCTGAAGTACTGTGC CGGGGCCATGAAAGAAGTAA 202–207 1.000 81.3
atpA-atpF_p2 atpA-atpF GCCTACCTGAAGTACTGTGC TAATATTGGCATGCTCGGGG 217–222 1.000 80.5
atpA-atpF_p3 atpA-atpF TCGCCTACCTGAAGTACTGT CGGGGCCATGAAAGAAGTAA 204–209 1.000 79.6
atpA-atpF_p4 atpA-atpF GCCTACCTGAAGTACTGTGC CGGTGCTAATATTGGCATGC 223–228 1.000 79.3
atpA-atpF_p5 atpA-atpF CTACCTGAAGTACTGTGCCG CGGGGCCATGAAAGAAGTAA 200–205 1.000 79.1
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA GGGGGCGAAGTGATACAAAA 1441–1447 1.000 74.4
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA CAATCCAAAACAAAGGGGGC 1455–1461 1.000 74.3
atpF_p3 atpF AATTTCGTCGGCTCGAATGG GGGGGCGAAGTGATACAAAA 1438–1444 1.000 71.6
atpF_p4 atpF AATTTCGTCGGCTCGAATGG CAATCCAAAACAAAGGGGGC 1452–1458 1.000 71.5
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA CAAAGGGGGCGAAGTGATAC 1445–1451 1.000 70.8
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAACGCAGTAGCA AGTTCAATCGGTCAGAGCAC 1106–1148 1.000 71.5
psbM-trnD-GUC_p2 psbM-trnD-GUC GAATGAACAACGCAGTAGCA AGTTCAATCGGTCAGAGCAC 1105–1147 1.000 71.4
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAACGCAGTAGCA ATGCTGTACACCCCATTTCC 1135–1177 1.000 71.0
psbM-trnD-GUC_p4 psbM-trnD-GUC GAATGAACAACGCAGTAGCA ATGCTGTACACCCCATTTCC 1134–1176 1.000 70.9
psbM-trnD-GUC_p5 psbM-trnD-GUC GAATGAACAACGCAGTAGCAA AGTTCAATCGGTCAGAGCAC 1105–1147 1.000 69.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (22)

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

Species Accession Length (bp) Link
Machilus balansae NC_028074.1 152721 View on NCBI ↗
Machilus bonii NC_058710.1 152641 View on NCBI ↗
Machilus calcicola NC_058711.1 152628 View on NCBI ↗
Machilus chayuensis NC_058712.1 152600 View on NCBI ↗
Machilus chekiangensis NC_058713.1 152623 View on NCBI ↗
Machilus duthiei MT621635.1 152595 View on NCBI ↗
Machilus faberi NC_058715.1 152637 View on NCBI ↗
Machilus gamblei NC_058716.1 152589 View on NCBI ↗
Machilus grijsii NC_058717.1 152647 View on NCBI ↗
Machilus leptophylla NC_056917.1 152624 View on NCBI ↗
Machilus lichuanensis NC_058718.1 152618 View on NCBI ↗
Machilus melanophylla NC_058719.1 152719 View on NCBI ↗
Machilus minutiflorus NC_058690.1 152654 View on NCBI ↗
Machilus nanmu PQ346899.1 152618 View on NCBI ↗
Machilus oreophila NC_058721.1 152684 View on NCBI ↗
Machilus platycarpa OR264254.1 152653 View on NCBI ↗
Machilus pomifera OR264255.1 152676 View on NCBI ↗
Machilus robusta NC_057619.1 152737 View on NCBI ↗
Machilus rufipes MT621629.1 152626 View on NCBI ↗
Machilus tenuipilis NC_058722.1 152660 View on NCBI ↗
Machilus versicolora NC_058723.1 152609 View on NCBI ↗
Machilus yunnanensis NC_028073.1 152622 View on NCBI ↗