Markers + reference

Polygala

7 species · Polygalaceae · Fabales

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Species 7
Genome length 164–165 kb
Candidate markers 279
Primer pairs 95

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 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 275 0.0698 0.95 72.0 yes View details
trnI-AAU-ndhC LSC 599 0.0650 0.83 77.1 yes View details
trnL-UAA-trnQ-UUG LSC 701 0.0432 0.98 80.5 yes View details
trnS-GCU-trnG-UCC LSC 858 0.0435 0.99 82.3 yes View details
atpH-atpI LSC 1371 0.0384 0.98 85.6 yes View details
ndhF SSC 2241 0.0408 1.00 74.0 yes View details
ndhF-rpl32 SSC 456 0.0751 0.97 81.7 yes View details
ccsA-ndhD SSC 321 0.0789 0.95 72.1 yes View details
ndhE SSC 306 0.0146 1.00 45.1 yes View details
trnG-UCC-trnR-UCU LSC 225 0.0453 0.99 81.4 yes View details
atpF-atpH LSC 442 0.0395 1.00 79.9 yes View details
trnQ-UUG-psbK LSC 636 0.0400 0.98 79.6 yes View details
infA-rps8 LSC 128 0.0767 1.00 78.4 yes View details
ndhG-ndhI IRa 279 0.0711 0.96 76.9 yes View details
atpE-trnM-CAU LSC 324 0.0699 0.90 76.6 yes View details
ndhE-ndhG SSC 193 0.1007 0.99 76.5 yes View details
ndhI-ndhF IRb 225 0.0786 0.95 76.2 yes View details
ndhD-psaC SSC 131 0.0504 0.96 75.3 yes View details
psbJ-petA LSC 1019 0.0307 0.99 74.3 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.

Primer pairs

Showing the top 30 of 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA ATCCACTTGGCTACATCCG TGTAGAAGCTCCATCTATAAATGG 291–323 1.000 52.0
trnH-GUG-psbA_p2 trnH-GUG-psbA ATCCACTTGGCTACATCCGC TGTAGAAGCTCCATCTATAAATGG 291–323 1.000 52.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CCACTTGGCTACATCCGC TGTAGAAGCTCCATCTATAAATGG 289–321 1.000 52.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ATCCACTTGGCTACATCCG AGAAGCTCCATCTATAAATGG 288–320 1.000 52.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ATCCACTTGGCTACATCCGC AGAAGCTCCATCTATAAATGG 288–320 1.000 52.0
atpE-trnM-CAU_p1 atpE-trnM-CAU GATCCACAAGAAGCTCAGCA GACATAGGTCTGCTTCTGGC 1121–1162 0.857 81.0
atpE-trnM-CAU_p2 atpE-trnM-CAU TGATCCACAAGAAGCTCAGC GACATAGGTCTGCTTCTGGC 1122–1163 0.857 80.9
atpE-trnM-CAU_p3 atpE-trnM-CAU CATCGATGAAGCTACTGCGA GCTCCATGTGCTCTGATTCA 1514–1549 0.857 79.8
atpE-trnM-CAU_p4 atpE-trnM-CAU GATCCACAAGAAGCTCAGCA GCTCCATGTGCTCTGATTCA 1196–1231 0.714 73.9
atpE-trnM-CAU_p5 atpE-trnM-CAU TGATCCACAAGAAGCTCAGC GCTCCATGTGCTCTGATTCA 1197–1232 0.714 73.9
trnI-AAU-ndhC_p1 trnI-AAU-ndhC GGTTCGAATCCGTATAGCCC TGCCCAAAGAATATCATATTCGT 563–657 1.000 52.3
trnI-AAU-ndhC_p2 trnI-AAU-ndhC CGGTTCGAATCCGTATAGCC TGCCCAAAGAATATCATATTCGT 564–658 1.000 52.0
trnI-AAU-ndhC_p3 trnI-AAU-ndhC GGTTCGAATCCGTATAGCCC TCATATTCGTAAAGCAAAAGCA 550–644 1.000 52.0
trnI-AAU-ndhC_p4 trnI-AAU-ndhC GGTTCGAATCCGTATAGCCC ATGCCCAAAGAATATCATATTCGT 564–658 1.000 52.0
trnI-AAU-ndhC_p5 trnI-AAU-ndhC CGGTTCGAATCCGTATAGCC TCATATTCGTAAAGCAAAAGCA 551–645 1.000 52.0
trnL-UAA-trnQ-UUG_p1 trnL-UAA-trnQ-UUG ACCAATTTCGCCATATCCCC TTTTGGTCCCGCTATTCGAG 743–763 0.857 83.8
trnL-UAA-trnQ-UUG_p2 trnL-UAA-trnQ-UUG TAGCGTCTACCAATTTCGCC TTTTGGTCCCGCTATTCGAG 751–771 0.857 83.2
trnL-UAA-trnQ-UUG_p3 trnL-UAA-trnQ-UUG ACCAATTTCGCCATATCCCC GTTTTGGTCCCGCTATTCGA 744–764 0.857 81.8
trnL-UAA-trnQ-UUG_p4 trnL-UAA-trnQ-UUG AGTCCGTAGCGTCTACCAAT TTTTGGTCCCGCTATTCGAG 757–777 0.857 81.7
trnL-UAA-trnQ-UUG_p5 trnL-UAA-trnQ-UUG TAGCGTCTACCAATTTCGCC GTTTTGGTCCCGCTATTCGA 752–772 0.857 81.1
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CTCGAATAGCGGGACCAAAA ACCAATACAGATCAAACTAAAGA 709–719 0.857 43.6
trnQ-UUG-psbK_p2 trnQ-UUG-psbK TCGAATAGCGGGACCAAAAC ACCAATACAGATCAAACTAAAGA 708–718 0.857 43.6
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CTCGAATAGCGGGACCAAAA ACCAATACAGATCAAACTAAAGAT 709–719 0.857 43.6
trnQ-UUG-psbK_p4 trnQ-UUG-psbK TCGAATAGCGGGACCAAAAC ACCAATACAGATCAAACTAAAGAT 708–718 0.857 43.6
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AGTATGCTCTGGGACGGAAG ACCAATACAGATCAAACTAAAGA 739–749 0.857 43.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AGGAAGGAGGACCCCTTAAC 755–1134 1.000 87.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGAAGGAGGACCCCTTAACT 754–1133 1.000 87.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC AGGAAGGAGGACCCCTTAAC 750–1129 1.000 87.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGAAGGAGGACCCCTTAACT 749–1128 1.000 87.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT GGAAGGAGGACCCCTTAACT 750–1129 1.000 84.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Polygala alpestris subsp. alpestris PP541865.1 164201 View on NCBI ↗
Polygala crotalarioides MW543308.1 164268 View on NCBI ↗
Polygala hongkongensis NC_066219.1 165296 View on NCBI ↗
Polygala japonica NC_052912.1 165439 View on NCBI ↗
Polygala sibirica NC_056970.1 165397 View on NCBI ↗
Polygala subopposita NC_072134.1 164784 View on NCBI ↗
Polygala tenuifolia NC_050829.1 165423 View on NCBI ↗