Markers + reference

Pleuropterus

2 species · Polygonaceae · Caryophyllales

Back to catalogue

Species 2
Genome length 164–164 kb
Candidate markers 273
Primer pairs 85

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 6 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 1311 0.0015 1.00 59.6 yes View details
rpoC2 LSC 4077 0.0002 1.00 54.1 yes View details
rbcL LSC 1449 0.0000 1.00 29.0 yes View details
rbcL-accD LSC 485 0.0062 1.00 59.9 yes View details
ycf1 IRb 5628 0.0005 1.00 52.8 yes View details
ccsA SSC 966 0.0000 1.00 33.4 yes View details
ccsA-ndhD SSC 219 0.0457 1.00 78.8 yes View details
ndhD SSC 1578 0.0006 1.00 51.2 yes View details
rps15 SSC 264 0.0265 1.00 54.0 yes View details
rps15-ycf1 IRa 292 0.0840 0.86 73.5 yes View details
ycf1 IRa 5628 0.0005 1.00 47.9 no View details
trnW-CCA LSC 74 0.0135 1.00 60.3 yes View details
trnE-UUC-trnT-GGU LSC 914 0.0011 1.00 59.4 yes View details
ndhF-rpl32 SSC 1074 0.0009 1.00 59.3 yes View details
rps16 LSC 1133 0.0000 1.00 58.8 yes View details
rps16-trnQ-UUG LSC 1460 0.0000 1.00 58.8 yes View details
trnV-UAC-trnM-CAU LSC 176 0.0057 1.00 55.8 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 AGAGCAAAAAGGGTGGGAAT ACGTACCGACTAAACCAATGA 1306–1307 1.000 58.9
rps16_p2 rps16 AGAGCAAAAAGGGTGGGAAT TGTACGTACCGACTAAACCA 1309–1310 1.000 58.1
rps16_p3 rps16 AGAGCAAAAAGGGTGGGAAT CGTACCGACTAAACCAATGACT 1305–1306 1.000 57.2
rps16_p4 rps16 AGAGCAAAAAGGGTGGGAAT CGTACCGACTAAACCAATGAC 1305–1306 1.000 56.4
rps16_p5 rps16 AGAGCAAAAAGGGTGGGAAT TGTACGTACCGACTAAACCAA 1309–1310 1.000 56.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1532–1533 1.000 78.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACATCAGATCGTGTCCT GAGGTTCGAATCCTTCCGTC 1554–1555 1.000 78.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1546–1547 1.000 74.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACATCAGATCGTGTCCTT GAGGTTCGAATCCTTCCGTC 1553–1554 1.000 74.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1536–1537 1.000 73.6
trnG-UCC_p1 trnG-UCC CGTTGTTCGACAAAAGTTCCA ATGGACGCTTCTCATTACGA 962 1.000 59.0
trnG-UCC_p2 trnG-UCC CGTTGTTCGACAAAAGTTCCA TGGACGCTTCTCATTACGAT 961 1.000 59.0
trnG-UCC_p3 trnG-UCC TCGTTGTTCGACAAAAGTTCC ATGGACGCTTCTCATTACGA 963 1.000 56.8
trnG-UCC_p4 trnG-UCC TCGTTGTTCGACAAAAGTTCC TGGACGCTTCTCATTACGAT 962 1.000 56.8
trnG-UCC_p5 trnG-UCC CGTTGTTCGACAAAAGTTCCA TGGACGCTTCTCATTACGATT 961 1.000 56.8
atpF_p1 atpF TTCATCAGCTCGAAGGGTTG AGTTTTTGAATCCATTTTCGA 1513 1.000 40.1
atpF_p2 atpF TTCATCAGCTCGAAGGGTTG AGGAAATAGGTCAAGTAATACAACA 1483 1.000 40.1
atpF_p3 atpF TTCATCAGCTCGAAGGGTTG AGTTTTTGAATCCATTTTCGAT 1513 1.000 40.1
atpF_p4 atpF TTCATCAGCTCGAAGGGTTG AGTTTTTGAATCCATTTTCGATT 1513 1.000 40.1
atpF_p5 atpF GCTCGAAGGGTTGTCATGAG AGTTTTTGAATCCATTTTCGA 1506 1.000 40.1
rpoC2_p1 rpoC2 GGATGGTGCCACAATCTCTT CAGGAGCTAGAGGAAATGCC 270 1.000 77.2
rpoC2_p2 rpoC2 GGATGGTGCCACAATCTCTT AATGCCTCTCAGGTACACCA 256 1.000 76.5
rpoC2_p3 rpoC2 GGATGGTGCCACAATCTCTT ATGCCTCTCAGGTACACCAA 255 1.000 76.5
rpoC2_p4 rpoC2 GGATGGTGCCACAATCTCTT TGCCTCTCAGGTACACCAAT 254 1.000 76.5
rpoC2_p5 rpoC2 GGTTTGGGGACTCACAGAAA CAGGAGCTAGAGGAAATGCC 296 1.000 75.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 1017 1.000 77.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 996 1.000 77.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 996 1.000 77.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 975 1.000 77.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 993 1.000 77.3

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
Pleuropterus angulatus ON529970.1 163673 View on NCBI ↗
Pleuropterus multiflorus NC_041239.1 163773 View on NCBI ↗