Markers + reference

Hedyosmum

8 species · Chloranthaceae · Chloranthales

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Species 8
Genome length 158–159 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1936 0.0243 0.99 67.6 yes View details
psbM-trnD-GUC LSC 1135 0.0771 1.00 86.8 yes View details
trnT-UGU-trnL-UAA LSC 797 0.0226 0.98 72.5 yes View details
psaI-ycf4 LSC 451 0.0303 1.00 65.9 yes View details
rps19 LSC 279 0.0155 1.00 39.7 yes View details
rpl2 IRb 1486 0.0019 1.00 35.1 no View details
ndhD SSC 1503 0.0115 1.00 48.2 yes View details
ndhD-ccsA SSC 259 0.0516 1.00 68.3 yes View details
trnL-UAG-rpl32 SSC 719 0.0253 0.99 66.2 yes View details
rpl32-ndhF SSC 973 0.0313 0.99 71.2 yes View details
ndhF SSC 2226 0.0137 1.00 49.1 yes View details
rpl2 IRa 1486 0.0019 1.00 35.1 yes View details
psbB-psbT LSC 195 0.0361 0.99 74.3 yes View details
rpl14-rpl16 LSC 146 0.0447 0.94 74.1 yes View details
rps19-trnH-GUG IRb 174 0.1061 0.95 71.7 yes View details
atpF-atpH LSC 452 0.0290 1.00 71.3 yes View details
ycf3-trnS-GGA LSC 846 0.0175 1.00 69.3 yes View details
rps18-rpl20 LSC 269 0.0334 1.00 66.8 yes View details
psbK-psbI LSC 403 0.0245 0.99 63.8 yes View details
ycf4-cemA LSC 919 0.0158 1.00 62.7 yes View details
trnE-UUC-trnT-GGU LSC 668 0.0171 0.98 62.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 2005–2057 1.000 84.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 2009–2061 1.000 82.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 2011–2063 1.000 81.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 2019–2068 0.750 72.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 2023–2072 0.750 71.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGTCCCGGATCATT 517–538 1.000 80.5
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCCTCACGTCCAGGATTACG 529–550 1.000 79.8
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGATTACGTCCCGGATCATT 514–535 1.000 78.5
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT GGATTACGTCCCGGATCATT 515–536 1.000 78.5
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT GGATTACGTCCCGGATCATT 516–537 1.000 78.5
atpF-atpH_p1 atpF-atpH GATGGCCAATAACCCAAGGA AATTTACGGACTGGTCGTGG 554–573 1.000 81.5
atpF-atpH_p2 atpF-atpH GATGGCCAATAACCCAAGGA TCGTGGCATTAGCGCTTTTA 540–559 1.000 80.2
atpF-atpH_p3 atpF-atpH GCCAATAACCCAAGGAAACG AATTTACGGACTGGTCGTGG 550–569 1.000 80.0
atpF-atpH_p4 atpF-atpH TGGCCAATAACCCAAGGAAA AATTTACGGACTGGTCGTGG 552–571 1.000 79.5
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTTCCGGC AATTTACGGACTGGTCGTGG 575–594 1.000 78.8
psbM-trnD-GUC_p1 psbM-trnD-GUC TGCGAGAATATTGACTTCCA GTTCGAGCCCCGTCAGTC 1032–1200 1.000 52.0
psbM-trnD-GUC_p2 psbM-trnD-GUC GGAACTAGAATGAACAATGCAGT GTTCGAGCCCCGTCAGTC 1064–1232 1.000 52.0
psbM-trnD-GUC_p3 psbM-trnD-GUC ATGCGAGAATATTGACTTCCA GTTCGAGCCCCGTCAGTC 1033–1201 1.000 52.0
psbM-trnD-GUC_p4 psbM-trnD-GUC TGCGAGAATATTGACTTCCAT GTTCGAGCCCCGTCAGTC 1032–1200 1.000 52.0
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAATGCAGTAGC GTTCGAGCCCCGTCAGTC 1058–1226 1.000 52.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 741–771 1.000 85.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 720–750 1.000 85.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 720–750 1.000 84.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 699–729 1.000 84.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 717–747 1.000 84.7
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA CCCTCGGTAAACAAAAGCCT 990–1030 1.000 72.0
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA CCCTCGGTAAACAAAAGCCT 991–1031 1.000 72.0
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 1011–1051 1.000 71.4
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA ACGGAAAGAGAGGGATTCGA 1012–1052 1.000 71.4
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA TTCCAATGCTACGCCTTGAA 961–1001 1.000 71.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Hedyosmum bonplandianum PQ728888.1 158297 View on NCBI ↗
Hedyosmum brenesii PQ728889.1 159218 View on NCBI ↗
Hedyosmum goudotianum PQ728890.1 158198 View on NCBI ↗
Hedyosmum maximum PQ728891.1 158075 View on NCBI ↗
Hedyosmum mexicanum PQ728892.1 157557 View on NCBI ↗
Hedyosmum nutans PQ728893.1 159027 View on NCBI ↗
Hedyosmum orientale NC_086728.1 158010 View on NCBI ↗
Hedyosmum peruvianum PQ728895.1 158082 View on NCBI ↗