Markers + reference

Drypetes

6 species · Putranjivaceae · Malpighiales

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Species 6
Genome length 119–121 kb
Candidate markers 226
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 226 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD Genome 1092 0.0838 0.95 83.1 yes View details
accD-rbcL Genome 2975 0.2411 0.87 76.6 yes View details
rbcL-trnV-UAC Genome 794 0.0927 0.57 78.0 yes View details
trnK-UUU-trnQ-UUG Genome 831 0.0737 0.91 83.3 yes View details
psbZ-trnG-GCC Genome 710 0.0509 0.89 81.7 yes View details
rpl14-rps8 Genome 210 0.0543 0.97 81.5 yes View details
trnH-GUG-psbA Genome 437 0.0614 1.00 81.4 yes View details
ndhD-psaC Genome 139 0.0489 0.99 78.3 yes View details
trnR-UCU-atpA Genome 148 0.0881 0.95 77.6 yes View details
trnQ-UUG-psbK Genome 715 0.0551 0.78 77.4 yes View details
psbK-trnQ-UUG Genome 715 0.0540 0.77 77.2 yes View details
trnQ-UUG-ndhF Genome 99 0.0458 1.00 76.3 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TGACCACTTGGCTACATTCG CCTCTAGACCTAGCTGCTGT 197–523 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA TGACCACTTGGCTACATTCG TTCCCTCTAGACCTAGCTGC 200–526 1.000 90.7
trnH-GUG-psbA_p3 trnH-GUG-psbA TGACCACTTGGCTACATTCG TAGACCTAGCTGCTGTCGAA 193–519 1.000 90.3
trnH-GUG-psbA_p4 trnH-GUG-psbA TGACCACTTGGCTACATTCG CTAGACCTAGCTGCTGTCGA 194–520 1.000 88.6
trnH-GUG-psbA_p5 trnH-GUG-psbA TGACCACTTGGCTACATTCG TCTAGACCTAGCTGCTGTCG 195–521 1.000 88.6
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG GGACGAATCCGCTTCTTCAT GTTCGAAACCTTCCGTCCC 791–983 1.000 79.8
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG CCGATGGTATGGACGAATCC GTTCGAAACCTTCCGTCCC 801–993 1.000 79.7
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GTTCGAAACCTTCCGTCCC 740–932 1.000 78.9
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GTTCGAAACCTTCCGTCCC 739–931 1.000 78.9
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG GTTAGCCGCACTTAAAAGCC GTTCGAAACCTTCCGTCCC 754–946 1.000 78.2
trnQ-UUG-psbK_p1 trnQ-UUG-psbK ATAGGTATGCTCTGGGACGG AAGAGGACAGGGATTACGGG 595–1015 1.000 84.5
trnQ-UUG-psbK_p2 trnQ-UUG-psbK ATAGGTATGCTCTGGGACGG CAGGGATTACGGGCATAACA 588–1008 1.000 83.5
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ATAGGTATGCTCTGGGACGG ACAGGGATTACGGGCATAAC 589–1009 1.000 83.5
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AAGAGGACAGGGATTACGGG 550–970 1.000 82.3
trnQ-UUG-psbK_p5 trnQ-UUG-psbK ATAGGTATGCTCTGGGACGG TAGCAGCTTGCCAAACAAAG 627–1047 1.000 81.9
rpl14-rps8_p1 rpl14-rps8 ATTTTTGGTGCGATCCTCGA AGCCATGTCAGCATTTCGTA 338–377 1.000 82.4
rpl14-rps8_p2 rpl14-rps8 ATTTTTGGTGCGATCCTCGA TAGCCATGTCAGCATTTCGT 339–378 1.000 82.4
rpl14-rps8_p3 rpl14-rps8 TTTTTGGTGCGATCCTCGAG AGCCATGTCAGCATTTCGTA 337–376 1.000 78.8
rpl14-rps8_p4 rpl14-rps8 TTTTTGGTGCGATCCTCGAG TAGCCATGTCAGCATTTCGT 338–377 1.000 78.8
rpl14-rps8_p5 rpl14-rps8 ATTTTTGGTGCGATCCTCGA AGCCATGTCAGCATTTCGTAT 338–377 1.000 77.0
accD_p1 accD TTACGCCTGCATAAGAACCC CAAAAGGAAACGTCGAACCG 2090–2296 0.667 78.3
accD_p2 accD CCATTGCAATTGCCGGAAAT CAAAAGGAAACGTCGAACCG 1913–2168 0.667 77.8
accD_p3 accD CCATTGCAATTGCCGGAAAT TCGAGTTTGATCTGCTGAGC 1684 0.167 46.4
accD_p4 accD TTACGCCTGCATAAGAACCC TCGAGTTTGATCTGCTGAGC 1861 0.167 46.4
accD_p5 accD TTGCCGGAAATACTAAGCCC TCGAGTTTGATCTGCTGAGC 1675 0.167 46.3
accD-rbcL_p1 accD-rbcL CGACGTTTCCTTTTGAACCG TGCAGATACGGAGCTGGATA 494–549 0.333 55.8
accD-rbcL_p2 accD-rbcL CGGTTCGACGTTTCCTTTTG TGCAGATACGGAGCTGGATA 499–554 0.333 55.8
accD-rbcL_p3 accD-rbcL TTACAAAGAACAGCGGGCTT TGCAGATACGGAGCTGGATA 642–697 0.333 55.4
accD-rbcL_p4 accD-rbcL GCTCAGCAGATCAAACTCGA TGCAGATACGGAGCTGGATA 764 0.167 46.6
accD-rbcL_p5 accD-rbcL GCTCAGCAGATCAAACTCGA CTAAACGAGGGCATCCGAAA 639 0.167 46.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Drypetes chevalieri NC_051999.1 119720 View on NCBI ↗
Drypetes diopa NC_052000.1 119299 View on NCBI ↗
Drypetes hainanensis NC_052001.1 119105 View on NCBI ↗
Drypetes indica NC_052002.1 120596 View on NCBI ↗
Drypetes lateriflora NC_052003.1 120800 View on NCBI ↗
Drypetes longifolia NC_052004.1 119268 View on NCBI ↗