Markers + reference

Oplopanax

2 species · Araliaceae · Apiales

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Species 2
Genome length 156–156 kb
Candidate markers 266
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 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 1679 0.0018 0.99 59.9 yes View details
atpF LSC 1279 0.0016 1.00 59.6 yes View details
rps2 LSC 711 0.0000 1.00 27.0 yes View details
psbZ-trnG-UCC LSC 286 0.0000 0.99 53.5 yes View details
trnT-UGU-trnL-UAA LSC 682 0.0029 1.00 60.4 yes View details
rbcL-accD LSC 673 0.0045 1.00 61.3 yes View details
accD LSC 1530 0.0007 1.00 53.1 yes View details
trnN-GUU-ndhF IRb 1809 0.0022 1.00 47.2 yes View details
ndhF-rpl32 SSC 1184 0.0034 1.00 60.8 yes View details
trnE-UUC-trnT-GGU LSC 803 0.0013 0.99 60.3 yes View details
ccsA SSC 969 0.0021 1.00 59.9 yes View details
rps4 LSC 606 0.0016 1.00 59.7 yes View details
accD-psaI LSC 663 0.0015 1.00 59.6 yes View details
matK LSC 1518 0.0013 1.00 59.5 yes View details
petN-psbM LSC 774 0.0013 1.00 59.5 yes View details
psaA-ycf3 LSC 719 0.0014 1.00 59.5 yes View details
atpB-rbcL LSC 760 0.0013 1.00 59.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGTCCGTGTCAACCAATATCT TCAATGGTTTGATTGCCTTGTC 2785 1.000 46.2
trnK-UUU_p2 trnK-UUU TGTCCGTGTCAACCAATATCT CAATGGTTTGATTGCCTTGTCT 2784 1.000 46.2
trnK-UUU_p3 trnK-UUU TGTCCGTGTCAACCAATATCT TCAATGGTTTGATTGCCTTGT 2785 1.000 45.1
trnK-UUU_p4 trnK-UUU TGTCCGTGTCAACCAATATCT ATGGTTTGATTGCCTTGTCT 2782 1.000 44.3
trnK-UUU_p5 trnK-UUU TGTCCGTGTCAACCAATATCT TTCAATGGTTTGATTGCCTTGT 2786 1.000 42.8
matK_p1 matK TTACACGGATTCCTAACGAA CCTTGTTTTGACTGTATCGCA 1617 1.000 40.1
matK_p2 matK TTTACACGGATTCCTAACGA CCTTGTTTTGACTGTATCGCA 1618 1.000 40.1
matK_p3 matK TTACACGGATTCCTAACGAA ACCTTGTTTTGACTGTATCGC 1618 1.000 40.1
matK_p4 matK TTTACACGGATTCCTAACGA ACCTTGTTTTGACTGTATCGC 1619 1.000 40.1
matK_p5 matK TTACACGGATTCCTAACGAA CCTTGTTTTGACTGTATCGCAC 1617 1.000 40.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1743–1752 1.000 78.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1758–1767 1.000 77.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1757–1766 1.000 77.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1814–1823 1.000 75.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1747–1756 1.000 74.1
atpF_p1 atpF GGCTCGAATGGTTACCATGA AAAGAACGGGGGCAAAGTTA 1437 1.000 74.6
atpF_p2 atpF GGCTCGAATGGTTACCATGA AAAAAGAACGGGGGCAAAGT 1439 1.000 73.4
atpF_p3 atpF GGCTCGAATGGTTACCATGA AAAAGAACGGGGGCAAAGTT 1438 1.000 73.4
atpF_p4 atpF GGCTCGAATGGTTACCATGA AAGAACGGGGGCAAAGTTAT 1436 1.000 72.7
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA AAAGAACGGGGGCAAAGTTA 1449 1.000 72.0
rps2_p1 rps2 GCGCTCCTGACCAATTAGAA AATGGCTTGGGTCGTGTATC 1419–1421 1.000 79.6
rps2_p2 rps2 AAGCGCTCCTGACCAATTAG AATGGCTTGGGTCGTGTATC 1421–1423 1.000 79.6
rps2_p3 rps2 ACGTGAGTAAAGCCAAAGCA AATGGCTTGGGTCGTGTATC 1512–1514 1.000 79.5
rps2_p4 rps2 CTTCCACACCGGCTATATCG AATGGCTTGGGTCGTGTATC 1143–1145 1.000 79.3
rps2_p5 rps2 GCGCTCCTGACCAATTAGAA AGGCCTGAAAGAGAACGTTG 1746–1748 1.000 79.0
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 932–937 1.000 68.8
petN-psbM_p2 petN-psbM ACATTTTCCCTTTCGCTCGT TGCTACTGCACTGTTCATTCT 901–906 1.000 68.0
petN-psbM_p3 petN-psbM CCCTTTCGCTCGTAGTATGG TGCTACTGCACTGTTCATTCT 894–899 1.000 67.7
petN-psbM_p4 petN-psbM CCTTTCGCTCGTAGTATGGG TGCTACTGCACTGTTCATTCT 893–898 1.000 67.7
petN-psbM_p5 petN-psbM CTTTCGCTCGTAGTATGGGG TGCTACTGCACTGTTCATTCT 892–897 1.000 67.7

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
Oplopanax elatus NC_085753.1 156008 View on NCBI ↗
Oplopanax japonicus NC_082542.1 156135 View on NCBI ↗