Markers + reference

Persicaria

26 species · Polygonaceae · Caryophyllales

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Species 26
Genome length 158–161 kb
Candidate markers 266
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1069 0.0758 0.99 85.3 yes View details
trnS-GCU-trnG-UCC LSC 761 0.0633 0.93 80.0 yes View details
atpH-atpI LSC 636 0.0584 0.98 80.8 yes View details
petN-psbM LSC 846 0.0632 0.99 75.5 yes View details
trnE-UUC-trnT-GGU LSC 849 0.0627 0.98 78.1 yes View details
trnT-GGU-psbD LSC 1244 0.0528 0.90 77.8 yes View details
rps4-trnT-UGU LSC 641 0.0685 0.99 80.6 yes View details
trnW-CCA-trnP-UGG LSC 326 0.0918 0.67 62.1 yes View details
psaJ-rpl33 LSC 489 0.0719 1.00 78.1 yes View details
rpl32-trnL-UAG SSC 684 0.0931 0.92 77.4 yes View details
petA-psbJ LSC 735 0.0467 0.98 83.0 yes View details
trnT-UGU-trnL-UAA LSC 765 0.0575 0.97 82.9 yes View details
rpoB-trnC-GCA LSC 1261 0.0503 0.99 82.5 yes View details
ndhC-trnV-UAC LSC 1068 0.0594 0.99 82.3 yes View details
ycf3-trnS-GGA LSC 863 0.0538 1.00 80.9 yes View details
trnF-GAA-ndhJ LSC 593 0.0588 1.00 80.3 yes View details
psbM-trnD-GUC LSC 834 0.0528 0.99 80.1 yes View details
trnD-GUC-trnY-GUA LSC 410 0.0641 0.98 79.6 yes View details
trnK-UUU-rps16 LSC 722 0.0597 0.97 79.2 yes View details
psbK-psbI LSC 396 0.0619 0.99 79.2 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 GGTGTGGACGAATCCCTTAC AAAAGGGTATGTTGCTGCCA 1333–1639 1.000 91.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAGGGTATGTTGCTGCCA 1368–1674 1.000 91.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAAAGGGTATGTTGCTGCCA 1369–1675 1.000 91.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGGTATGTTGCTGCCA 1470–1678 0.846 85.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTTTCTTGAGCCGTACGAGG 1075–1281 0.846 85.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1073–1401 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1084–1412 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1077–1405 1.000 85.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1103–1431 1.000 85.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1085–1413 1.000 85.2
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGTCCCGGGTCATTAGA 471–538 1.000 90.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGTCCCGGGTCATTAGATA 469–536 1.000 88.6
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGTCCCGGGTCATTAGAT 470–537 1.000 88.6
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTACGTCCCGGGTCATTAGA 468–535 1.000 88.4
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTACGTCCCGGGTCATTAGA 469–536 1.000 88.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CACTCAGCCATCTCTCCCTA ACGAATCACACTTTTACCACT 720–840 1.000 63.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CACTCAGCCATCTCTCCCTA AGAACGAATCACACTTTTACCAC 723–843 1.000 62.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CACTCAGCCATCTCTCCCTA GAACGAATCACACTTTTACCACT 722–842 1.000 62.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CACTCAGCCATCTCTCCCTA AACGAATCACACTTTTACCACT 721–841 1.000 61.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CACTCAGCCATCTCTCCCTA TACCACTAAACTATACCCGC 706–826 1.000 59.3
atpH-atpI_p1 atpH-atpI CCTCATCCTCAAATCAGCCC TATCGTCCTTGGGTTCCCTT 1307–1581 1.000 91.5
atpH-atpI_p2 atpH-atpI CAGTGACCCAAGGAAACGAA TATCGTCCTTGGGTTCCCTT 1614–1842 0.923 88.3
atpH-atpI_p3 atpH-atpI ACGGAAGCGGCAGAAATAAT TATCGTCCTTGGGTTCCCTT 947–1159 0.692 78.4
atpH-atpI_p4 atpH-atpI TGCTAAAAGGCAAGCAGACA TATCGTCCTTGGGTTCCCTT 1231–1433 0.654 74.4
atpH-atpI_p5 atpH-atpI CTCATCCTCAAATCAGCCCC TATCGTCCTTGGGTTCCCTT 1492 0.038 41.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTCGACATTCCCTCACTTCC AAAGGATTTGCAGTCCTCCG 1010–1360 1.000 90.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GCCCAGGTATTGTCGACATT AAAGGATTTGCAGTCCTCCG 1181–1371 0.962 88.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCGACATTCCCTCACTTCCA AAAGGATTTGCAGTCCTCCG 1009–1359 1.000 87.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CATTCCCTCACTTCCAACCC AAAGGATTTGCAGTCCTCCG 1331 0.038 38.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGACATTCCCTCACTTCCAA AAAGGATTTGCAGTCCTCCG 1334 0.038 36.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (26)

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

Species Accession Length (bp) Link
Persicaria amphibia NC_071233.1 159455 View on NCBI ↗
Persicaria bungeana NC_082250.1 159660 View on NCBI ↗
Persicaria capitata NC_073007.1 158826 View on NCBI ↗
Persicaria criopolitana NC_079578.1 159441 View on NCBI ↗
Persicaria dissitiflora NC_082251.1 160982 View on NCBI ↗
Persicaria filiformis NC_058319.1 159741 View on NCBI ↗
Persicaria foliosa NC_082252.1 159693 View on NCBI ↗
Persicaria glabra NC_082253.1 159069 View on NCBI ↗
Persicaria glacialis NC_082254.1 158402 View on NCBI ↗
Persicaria hastatosagittata NC_082255.1 160798 View on NCBI ↗
Persicaria hydropiper NC_067040.1 159847 View on NCBI ↗
Persicaria kawagoeana NC_082256.1 159690 View on NCBI ↗
Persicaria lapathifolia NC_073006.1 159077 View on NCBI ↗
Persicaria lapathifolia var. salicifolia ON229580.1 159049 View on NCBI ↗
Persicaria longiseta NC_082257.1 159256 View on NCBI ↗
Persicaria longiseta var. rotundata ON229582.1 159401 View on NCBI ↗
Persicaria maculosa NC_082258.1 159076 View on NCBI ↗
Persicaria minor PQ275786.1 159897 View on NCBI ↗
Persicaria nepalensis NC_082259.1 157889 View on NCBI ↗
Persicaria paradoxa ON229600.1 159011 View on NCBI ↗
Persicaria pensylvanica PX373531.1 159036 View on NCBI ↗
Persicaria posumbu NC_082260.1 159350 View on NCBI ↗
Persicaria sagittata NC_082261.1 160422 View on NCBI ↗
Persicaria senticosa NC_067968.1 160804 View on NCBI ↗
Persicaria thunbergii NC_082262.1 159848 View on NCBI ↗
Persicaria viscofera NC_082263.1 159621 View on NCBI ↗