Markers + reference

Phoebe

21 species · Lauraceae · Laurales

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Species 21
Genome length 153–153 kb
Candidate markers 258
Primer pairs 100

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 Genome 394 0.0100 1.00 61.0 yes View details
atpA Genome 1524 0.0019 1.00 31.3 yes View details
petA-psbJ Genome 1152 0.0111 1.00 64.3 yes View details
ycf2 Genome 6858 0.0018 1.00 49.9 yes View details
ndhF Genome 2229 0.0026 1.00 35.5 yes View details
ndhF-rpl32 Genome 1235 0.0051 0.99 65.1 yes View details
rpl32-trnL-UAG Genome 1389 0.0046 1.00 55.6 yes View details
ccsA-ndhD Genome 241 0.0117 1.00 42.2 yes View details
ycf1 Genome 5565 0.0030 1.00 45.1 yes View details
rpl2-rpl23 Genome 33 0.0364 0.97 68.3 yes View details
psbM-trnD-GUC Genome 993 0.0025 1.00 54.4 yes View details
trnF-GAA-ndhJ Genome 567 0.0030 0.97 54.4 yes View details
rpl20-rps12 Genome 757 0.0019 1.00 52.6 yes View details
trnT-GGU-psbD Genome 1457 0.0016 0.99 52.3 yes View details
psbE-petL Genome 1243 0.0020 1.00 52.2 yes View details
ndhC-trnV-UAC Genome 1854 0.0025 1.00 51.7 yes View details
atpF Genome 1282 0.0015 1.00 51.4 yes View details
petN-psbM Genome 1062 0.0037 1.00 51.1 yes View details
ycf3 Genome 1971 0.0018 1.00 49.7 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 TTCCCTCTAGACCTAGCTGC 452–473 1.000 86.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 466–487 1.000 85.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 465–486 1.000 85.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 467–488 1.000 85.8
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 481–502 1.000 83.0
trnG-UCC_p1 trnG-UCC AACATGTCAGCACCCCAATT AGGGACATATCAAAAGCATGT 970–974 1.000 51.4
trnG-UCC_p2 trnG-UCC ACATGTCAGCACCCCAATTT AGGGACATATCAAAAGCATGT 969–973 1.000 51.4
trnG-UCC_p3 trnG-UCC TGTCAGCACCCCAATTTTCA AGGGACATATCAAAAGCATGT 966–970 1.000 50.9
trnG-UCC_p4 trnG-UCC AACATGTCAGCACCCCAATT TCCGATTTCTTTCACATTCTGAC 1046–1050 1.000 50.5
trnG-UCC_p5 trnG-UCC ACATGTCAGCACCCCAATTT TCCGATTTCTTTCACATTCTGAC 1045–1049 1.000 50.5
atpA_p1 atpA AGCCTTCCAAGCTAACGATG TAATCAGGTGCGACAACGAG 2083–2089 1.000 81.4
atpA_p2 atpA GTGCATTCAGACGAAAAGGC TAATCAGGTGCGACAACGAG 2320–2325 1.000 81.4
atpA_p3 atpA TCAGCTCGGTGGAACAAAAA TAATCAGGTGCGACAACGAG 2452–2457 1.000 81.3
atpA_p4 atpA ATCGGGACCATTTCTCAACG TAATCAGGTGCGACAACGAG 1786–1790 0.952 78.1
atpA_p5 atpA CGGGACCATTTCTCAACGAT TAATCAGGTGCGACAACGAG 1784–1788 0.857 74.3
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA GGGGGCGAAGTGATACAAAA 1438–1448 1.000 75.3
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA CAATCCAAAACAAAGGGGGC 1452–1462 1.000 75.2
atpF_p3 atpF AATTTCGTCGGCTCGAATGG GGGGGCGAAGTGATACAAAA 1435–1445 1.000 72.5
atpF_p4 atpF AATTTCGTCGGCTCGAATGG CAATCCAAAACAAAGGGGGC 1449–1459 1.000 72.3
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA CAAAGGGGGCGAAGTGATAC 1442–1452 1.000 71.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGTTGTTCATTCT 1224–1225 1.000 70.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGTTGTTCATTC 1224–1225 1.000 70.2
petN-psbM_p3 petN-psbM GGGACACGATTCACATGGAT TGCTACTGCGTTGTTCATTCT 1245–1246 1.000 68.9
petN-psbM_p4 petN-psbM GGGACACGATTCACATGGAT TGCTACTGCGTTGTTCATTC 1245–1246 1.000 68.8
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCGTTGTTCATTCT 1163–1164 1.000 68.7
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAACGCAGTAGCA AGTTCAATCGGTCAGAGCAC 1084–1129 1.000 73.3
psbM-trnD-GUC_p2 psbM-trnD-GUC GAATGAACAACGCAGTAGCA AGTTCAATCGGTCAGAGCAC 1083–1128 1.000 73.2
psbM-trnD-GUC_p3 psbM-trnD-GUC GAATGAACAACGCAGTAGCAA AGTTCAATCGGTCAGAGCAC 1083–1128 1.000 70.9
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAACGCAGTAGCA ATGCTGTACACCCCATTTCC 1114–1158 0.952 70.6
psbM-trnD-GUC_p5 psbM-trnD-GUC GAATGAACAACGCAGTAGCA ATGCTGTACACCCCATTTCC 1113–1157 0.952 70.5

Result downloads

candidate_marker_features.tsv primers.tsv

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
Phoebe calcarea NC_058725.1 152851 View on NCBI ↗
Phoebe cavaleriei NC_058724.1 152728 View on NCBI ↗
Phoebe crassipedicella NC_058726.1 152784 View on NCBI ↗
Phoebe formosana NC_058727.1 152698 View on NCBI ↗
Phoebe glaucophylla NC_058728.1 152859 View on NCBI ↗
Phoebe hui NC_067976.1 152837 View on NCBI ↗
Phoebe hunanensis NC_058689.1 152791 View on NCBI ↗
Phoebe jingxiensis PX363578.1 152788 View on NCBI ↗
Phoebe jinpingensis PX297391.1 152810 View on NCBI ↗
Phoebe kwangsiensis PX297393.1 152785 View on NCBI ↗
Phoebe lanceolata NC_058729.1 152809 View on NCBI ↗
Phoebe legendrei PX297401.1 152744 View on NCBI ↗
Phoebe macrocarpa NC_058730.1 152750 View on NCBI ↗
Phoebe neurantha NC_039620.1 152782 View on NCBI ↗
Phoebe neuranthoides NC_058731.1 152880 View on NCBI ↗
Phoebe omeiensis NC_031190.1 152855 View on NCBI ↗
Phoebe panzhihuaensis PX297395.1 152537 View on NCBI ↗
Phoebe puwenensis NC_050171.1 152746 View on NCBI ↗
Phoebe sheareri NC_031191.1 152876 View on NCBI ↗
Phoebe yunnanensis MT621606.1 152833 View on NCBI ↗
Phoebe zhennan NC_036143.1 152831 View on NCBI ↗