Markers + reference

Koenigia

10 species · Polygonaceae · Caryophyllales

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Species 10
Genome length 154–159 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 850 0.0820 0.94 75.2 yes View details
trnS-GCU-trnG-UCC LSC 620 0.1216 0.97 75.2 yes View details
rpoB-trnC-GCA LSC 1237 0.0743 0.99 76.4 yes View details
petN-psbM LSC 583 0.0922 0.99 85.9 yes View details
psbM-trnD-GUC LSC 1183 0.0708 0.97 78.8 yes View details
trnE-UUC-trnT-GGU LSC 852 0.1085 0.97 84.1 yes View details
trnT-UGU-trnL-UAA LSC 740 0.0968 0.98 74.7 yes View details
ndhC-trnV-UAC LSC 893 0.0900 0.98 84.5 yes View details
rpl33-rps18 LSC 445 0.1114 0.81 68.8 yes View details
ndhF-rpl32 SSC 985 0.0723 0.60 70.9 yes View details
rpl32-trnL-UAG SSC 758 0.1448 0.91 78.3 yes View details
psbE-petL LSC 621 0.0604 1.00 82.8 yes View details
ycf3-trnS-GGA LSC 876 0.0645 0.92 82.2 yes View details
trnR-ACG-trnN-GUU IRb 610 0.0375 1.00 81.9 yes View details
trnN-GUU-trnR-ACG IRa 610 0.0376 1.00 81.9 yes View details
petA-psbJ LSC 710 0.0671 1.00 79.6 yes View details
ndhA SSC 2156 0.0605 0.99 79.1 yes View details
clpP LSC 2200 0.0528 0.98 78.5 yes View details
atpF LSC 1334 0.0447 0.99 78.2 yes View details
rps4-trnT-UGU LSC 626 0.0729 0.91 77.8 yes View details
psaJ-rpl33 LSC 456 0.0829 0.90 77.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT CTTACAGCAGCTTGCCAAAC 1687–1915 1.000 91.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT TTTGGGCTGGAATTGACGAA 1329–1435 0.500 71.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCCACACCAGATCATGTCCT TTTGGGCTGGAATTGACGAA 966–1059 0.500 71.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TAACCCCCTTTTTGTCTGGC TTTGGGCTGGAATTGACGAA 1600 0.200 47.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TAACCCCCTTTTTGTCTGGC CTTACAGCAGCTTGCCAAAC 2065 0.200 47.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GTTTGGCAAGCTGCTGTAAG CATCGTTAGCTTGGAAGGCT 2024–2047 0.600 74.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GTTTGGCAAGCTGCTGTAAG CTCGCTTGCTAGATGATCCC 1822–1845 0.600 74.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GTTTGGCAAGCTGCTGTAAG CGTTAGCTTGGAAGGCTAGG 2021–2044 0.600 74.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GTTTGGCAAGCTGCTGTAAG AGAATATGCCGCTCGATGAC 1705–1719 0.400 62.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GTTTGGCAAGCTGCTGTAAG GAATATGCCGCTCGATGACT 1704 0.200 47.0
atpF_p1 atpF TGACTACCTGTGCTACCGAA ATTTCTGCCGCTTCCGTTAT 2649–2706 0.700 76.6
atpF_p2 atpF CTGTGCTACCGAAGATGCTT ATTTCTGCCGCTTCCGTTAT 2535–2699 0.600 71.8
atpF_p3 atpF CTGTGCTACCGAAGATGCTT AGGCCAAGCTGTAGAAGGTA 2452–2616 0.600 71.8
atpF_p4 atpF ACCAGTCTGTCTGTCTCCAA ATTTCTGCCGCTTCCGTTAT 2436–2600 0.600 71.2
atpF_p5 atpF TGACTACCTGTGCTACCGAA AGGCCAAGCTGTAGAAGGTA 2577–2623 0.500 67.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCAGATTTGAACCGGGGAAA 1738–1919 1.000 91.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AATAGTGAAATCCGGGGTGC 2220–2484 0.800 83.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA AATAGTGAAATCCGGGGTGC 1804–2068 0.800 83.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTCACCACCTACACAAGCAA AATAGTGAAATCCGGGGTGC 2416–2680 0.800 83.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAATACCGGGTCACCACCTA AATAGTGAAATCCGGGGTGC 2425–2689 0.800 83.2
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT AAAACGGTCAGTCAAAACGA 646–707 1.000 75.9
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AAAACGGTCAGTCAAAACGA 585–646 1.000 74.3
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT AAACGGTCAGTCAAAACGAT 645–706 1.000 74.1
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT AACGGTCAGTCAAAACGATT 644–705 1.000 74.1
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT AAAAACGGTCAGTCAAAACGA 647–708 1.000 73.9
psbM-trnD-GUC_p1 psbM-trnD-GUC ACTGTTGATTCTAGCCTGCG GGCCCAAGAATTCGCTCATA 1773–1853 0.700 79.6
psbM-trnD-GUC_p2 psbM-trnD-GUC CTGTTGATTCTAGCCTGCGT GGCCCAAGAATTCGCTCATA 1772–1852 0.700 79.6
psbM-trnD-GUC_p3 psbM-trnD-GUC GCAGGGCTTTTCTCAGACTT GGCCCAAGAATTCGCTCATA 2128–2138 0.400 59.6
psbM-trnD-GUC_p4 psbM-trnD-GUC CTGTTGATTCTAGCCTGCGT GTCTTACCGAACGCACGATA 1801–1811 0.400 58.9
psbM-trnD-GUC_p5 psbM-trnD-GUC CTGTTGATTCTAGCCTGCGT TCTTACCGAACGCACGATAC 1800–1810 0.400 58.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Koenigia alpina NC_066667.1 159135 View on NCBI ↗
Koenigia campanulata var. fulvida MZ573784.1 154446 View on NCBI ↗
Koenigia cyanandra NC_066668.1 155971 View on NCBI ↗
Koenigia divaricata NC_066669.1 159126 View on NCBI ↗
Koenigia forrestii NC_066670.1 156798 View on NCBI ↗
Koenigia islandica NC_066671.1 155854 View on NCBI ↗
Koenigia lichiangensis NC_066672.1 154524 View on NCBI ↗
Koenigia mollis var. mollis MZ573793.1 158578 View on NCBI ↗
Koenigia mollis var. rudis MZ573794.1 158627 View on NCBI ↗
Koenigia nepalensis NC_066673.1 155838 View on NCBI ↗