Markers + reference

Pteroxygonum

2 species · Polygonaceae · Caryophyllales

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Species 2
Genome length 162–163 kb
Candidate markers 263
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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 341 0.1234 0.90 78.2 yes View details
rps16-trnQ-UUG LSC 1391 0.0627 0.83 76.2 yes View details
trnS-GCU-trnG-UCC LSC 907 0.0755 0.96 86.3 yes View details
trnE-UUC-trnT-GGU LSC 900 0.0460 0.94 75.6 yes View details
trnS-UGA-psbZ LSC 329 0.0396 1.00 66.0 yes View details
ycf3-trnS-GGA LSC 940 0.0475 0.94 79.5 yes View details
rps4-trnT-UGU LSC 694 0.0874 0.78 80.9 yes View details
ndhC-trnV-UAC LSC 1129 0.0546 0.88 78.3 yes View details
ndhF-rpl32 SSC 988 0.0558 0.98 78.6 yes View details
rpl32-trnL-UAG SSC 534 0.0625 0.96 77.4 yes View details
ndhA SSC 2129 0.0299 0.97 63.0 yes View details
psbI-trnS-GCU LSC 116 0.1053 0.98 82.2 yes View details
rpl20-rps12 LSC 779 0.0342 0.98 80.6 yes View details
psbT-psbN LSC 71 0.0704 1.00 80.1 yes View details
trnR-UCU-atpA LSC 156 0.0897 0.93 76.6 yes View details
psbM-trnD-GUC LSC 1139 0.0419 0.99 75.7 yes View details
psbE-petL LSC 1192 0.0379 0.97 75.6 yes View details
trnC-GCA-petN LSC 837 0.0398 0.96 74.5 yes View details
rpl2-rpl23 IRb 19 0.0556 0.95 74.3 yes View details
rpoB-trnC-GCA LSC 1311 0.0369 0.97 74.2 yes View details
ycf4-cemA LSC 747 0.0385 0.97 73.6 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 GCGCTAACCTTGGTATGGAA 457–465 1.000 89.6
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGTTGCGTATTCAGCTCCT 994–1002 1.000 84.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTGTTGCGTATTCAGCTCCT 1008–1016 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTGTTGCGTATTCAGCTCCT 1007–1015 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTGTTGCGTATTCAGCTCCT 1009–1017 1.000 84.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT CTTACAGCAGCTTGCCAAAC 2156–2367 1.000 86.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGGAAACTTGGTGGGATTGG CTTACAGCAGCTTGCCAAAC 2308 0.500 59.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGGATTGGAAACTTGGTGGG CTTACAGCAGCTTGCCAAAC 2313 0.500 59.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGAAACTTGGTGGGATTGG GAGGTTCGAATCCTTCCGTC 1749 0.500 59.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGGATTGGAAACTTGGTGGG GAGGTTCGAATCCTTCCGTC 1754 0.500 59.3
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTCATTCGTACCGAGGGTTC 177 1.000 78.2
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATAGATGGCTGAGTGGACGA 226 1.000 76.9
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TAGATGGCTGAGTGGACGAA 225 1.000 76.3
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA AGGGATAGATGGCTGAGTGG 230 1.000 75.2
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGGATAGATGGCTGAGTGGA 229 1.000 75.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCGTCCACTCAGCCATCTAT CGGATTAGGAATCGAAGGATCC 1000 0.500 42.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCGTCCACTCAGCCATCTAT GGATTAGGAATCGAAGGATCCC 999 0.500 41.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CGGATTAGGAATCGAAGGATCC 1067 0.500 41.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TTCGTCCACTCAGCCATCTA CGGATTAGGAATCGAAGGATCC 1001 0.500 41.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGATTAGGAATCGAAGGATCCC 1066 0.500 41.1
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGAGAAGCGTCCATTGTCT GGAACGTTTTCTACTTCAGGA 250–260 1.000 51.5
trnR-UCU-atpA_p2 trnR-UCU-atpA ATCGTAATGAGAAGCGTCCA GGAACGTTTTCTACTTCAGGA 256–266 1.000 49.9
trnR-UCU-atpA_p3 trnR-UCU-atpA TCGTAATGAGAAGCGTCCAT GGAACGTTTTCTACTTCAGGA 255–265 1.000 49.9
trnR-UCU-atpA_p4 trnR-UCU-atpA ATGAGAAGCGTCCATTGTCT GGAACGTTTTCTACTTCAGGAA 250–260 1.000 49.5
trnR-UCU-atpA_p5 trnR-UCU-atpA AATGAGAAGCGTCCATTGTCT GGAACGTTTTCTACTTCAGGA 251–261 1.000 49.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GCCCAGGTATTGTCGACATT CCAGATTTGAACCGGGGAAA 1380–1417 1.000 83.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA CCAGATTTGAACCGGGGAAA 1433–1470 1.000 83.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GCCCAGGTATTGTCGACATT AAAGGATTTGCAGTCCTCCG 1360–1397 1.000 83.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA AAAGGATTTGCAGTCCTCCG 1413–1450 1.000 83.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC CCAGATTTGAACCGGGGAAA 1443–1480 1.000 80.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Pteroxygonum denticulatum NC_068877.1 162897 View on NCBI ↗
Pteroxygonum giraldii NC_082272.1 162009 View on NCBI ↗