Markers + reference

Polygonum

12 species · Polygonaceae · Caryophyllales

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Species 12
Genome length 159–163 kb
Candidate markers 266
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 336 0.0929 1.00 63.5 yes View details
trnK-UUU-rps16 LSC 972 0.0526 0.99 73.2 yes View details
trnS-GCU-trnG-UCC LSC 1176 0.0416 1.00 72.6 yes View details
rpoB-trnC-GCA LSC 1349 0.0452 0.99 73.9 yes View details
trnC-GCA-petN LSC 672 0.0528 1.00 73.7 yes View details
trnE-UUC-trnT-GGU LSC 837 0.0615 1.00 77.8 yes View details
rps4-trnT-UGU LSC 590 0.0676 0.99 72.5 yes View details
trnT-UGU-trnL-UAA LSC 524 0.0632 1.00 72.5 yes View details
trnF-GAA-ndhJ LSC 675 0.0577 1.00 71.0 yes View details
ndhC-trnV-UAC LSC 542 0.0947 1.00 69.8 yes View details
rpl33-rps18 LSC 516 0.0627 0.99 70.7 yes View details
rpl32-trnL-UAG SSC 685 0.0785 1.00 75.4 yes View details
atpH-atpI LSC 676 0.0457 0.98 73.6 yes View details
ycf4-cemA LSC 861 0.0486 1.00 73.1 yes View details
trnT-GGU-psbD LSC 1537 0.0431 0.99 72.5 yes View details
psbZ-trnG-GCC LSC 283 0.0767 1.00 72.1 yes View details
ndhF-rpl32 SSC 929 0.0425 1.00 71.4 yes View details
psaJ-rpl33 LSC 563 0.0515 1.00 71.3 yes View details
trnL-UAA-trnF-GAA LSC 367 0.0494 1.00 69.5 yes View details
psbM-trnD-GUC LSC 1229 0.0347 1.00 69.2 yes View details
petN-psbM LSC 1173 0.0407 1.00 68.6 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 105 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 CTGTTGCGTATTCAGCTCCT 948–1003 1.000 90.8
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATTTCAGGCTGAGCACAACA 864–879 0.833 72.5
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTTCAGGCTGAGCACAACAT 863–878 0.833 72.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ATTTCAGGCTGAGCACAACA 878–893 0.833 72.4
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTTCAGGCTGAGCACAACAT 877–892 0.833 72.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTTTCTTGAGCCGTACGAGG 1214–1391 1.000 91.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1205–1382 1.000 91.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTATCCCAATGAGCCGTCT 1147–1327 1.000 91.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA TTTTCTTGAGCCGTACGAGG 1167–1344 1.000 91.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA GCCGTACGAGGAGAAAACTT 1158–1335 1.000 91.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 766–1281 1.000 55.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC AGAACGAATCACACTTTTACCAC 769–1284 1.000 53.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC GAACGAATCACACTTTTACCACT 768–1283 1.000 53.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC AACGAATCACACTTTTACCACT 767–1282 1.000 53.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GTCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 767–1282 1.000 52.0
atpH-atpI_p1 atpH-atpI CCTCGTATTTTCCCCTCTGC GCTGCTCGAAATCCACAAAC 1384–1404 0.833 74.7
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT GCTGCTCGAAATCCACAAAC 1347–1367 0.833 74.7
atpH-atpI_p3 atpH-atpI TTCCCCCAGTTTTCTCAACG GCTGCTCGAAATCCACAAAC 1603–1623 0.833 74.6
atpH-atpI_p4 atpH-atpI TTCCCCCAGTTTTCTCAACG TATCGTCCTTGGGTTCCCTT 1501–1521 0.833 74.6
atpH-atpI_p5 atpH-atpI TTCCCCCAGTTTTCTCAACG CTTATTAAGCTCAGCCGCCA 1625–1645 0.833 74.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GCCCAGGTATTGTCGACATT CGAATCAAGCGCGTATCAAC 1533–1554 0.833 75.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCAAATTAACCCCGCGGATA CGAATCAAGCGCGTATCAAC 1754–1775 0.833 75.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCGACCCCATAGCTGATGAT CGAATCAAGCGCGTATCAAC 2058–2079 0.833 74.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TAGACTCGACCCCATAGCTG CGAATCAAGCGCGTATCAAC 2063–2084 0.833 74.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CGAATCAAGCGCGTATCAAC 2002–2023 0.833 74.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG AGCCCAAGCGAGACTTACTA 728–877 1.000 87.9
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG GCCCAAGCGAGACTTACTAT 727–876 1.000 82.0
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG ATTAAAGCAGCCCAAGCGAG 736–885 1.000 81.9
trnC-GCA-petN_p4 trnC-GCA-petN CCGGTTCAAATCTGGGTGTC AGCCCAAGCGAGACTTACTA 723–872 1.000 81.9
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCGGTTCAAATCTGG GACTACCATTAAAGCAGCCCA 743–892 1.000 81.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Polygonum argyrocoleon NC_082264.1 163236 View on NCBI ↗
Polygonum aviculare NC_058892.1 163448 View on NCBI ↗
Polygonum aviculare subsp. aviculare PP541866.1 163440 View on NCBI ↗
Polygonum aviculare var. fusco-ochreatum ON229564.1 163274 View on NCBI ↗
Polygonum humifusum NC_082266.1 163274 View on NCBI ↗
Polygonum milletii NC_082239.1 159068 View on NCBI ↗
Polygonum patulum NC_082268.1 163361 View on NCBI ↗
Polygonum plebeium NC_063678.1 163461 View on NCBI ↗
Polygonum rigidum NC_082269.1 163456 View on NCBI ↗
Polygonum suffultum NC_082242.1 159115 View on NCBI ↗
Polygonum tachengense NC_082270.1 163402 View on NCBI ↗
Polygonum urumqiense NC_082271.1 163376 View on NCBI ↗