Markers + reference

Hymenopus

2 species · Chrysobalanaceae · Malpighiales

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Species 2
Genome length 163–163 kb
Candidate markers 268
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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 405 0.0631 0.98 87.1 yes View details
trnS-GCU-trnG-GCC LSC 946 0.0127 1.00 66.3 yes View details
trnG-GCC-trnR-UCU LSC 749 0.0150 0.89 61.6 yes View details
trnE-UUC-trnT-GGU LSC 671 0.0181 0.99 70.1 yes View details
trnT-GGU-psbD LSC 1607 0.0096 0.97 57.5 yes View details
psbZ-trnG-UCC LSC 701 0.0231 0.99 69.0 yes View details
psbE-petL LSC 1444 0.0140 0.99 52.9 yes View details
rpl33-rps18 LSC 298 0.0341 0.89 63.0 yes View details
rpl16 LSC 1514 0.0089 0.96 53.0 yes View details
ycf1 IRb 1105 0.0000 1.00 36.6 no View details
ycf1 SSC 5748 0.0065 1.00 56.5 yes View details
ndhF-rpl32 SSC 1109 0.0113 0.95 69.6 yes View details
ndhC-trnV-UAC LSC 1148 0.0135 0.97 69.2 yes View details
petA-psbJ LSC 853 0.0101 0.93 67.9 yes View details
ndhG-ndhI SSC 463 0.0091 0.95 65.7 yes View details
rpl20-rps12 LSC 824 0.0110 1.00 65.5 yes View details
psbJ-psbL LSC 180 0.0222 1.00 65.3 yes View details
trnF-GAA-ndhJ LSC 828 0.0025 0.95 65.0 yes View details
clpP-psbB LSC 481 0.0146 1.00 64.9 yes View details
trnC-GCA-petN LSC 957 0.0096 0.98 64.3 yes View details
trnR-ACG-trnN-GUU IRb 631 0.0095 1.00 64.2 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 CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 531–540 1.000 81.3
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 532–541 1.000 81.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 532–541 1.000 80.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 533–542 1.000 80.6
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 524–533 1.000 79.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGGGATCCCTTAACTATTAGGCT 1046–1066 1.000 56.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AGGGATCCCTTAACTATTAGGCT 1045–1065 1.000 56.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATCAACGGAACCGGAAAGAG AGGGATCCCTTAACTATTAGGCT 1110–1130 1.000 55.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGCAATCCGACGCTTTAGTC AGGGATCCCTTAACTATTAGGCT 1048–1068 1.000 53.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CGACGCTTTAGTCCACTCAG AGGGATCCCTTAACTATTAGGCT 1041–1061 1.000 53.2
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 747–829 1.000 68.4
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 750–832 1.000 68.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 753–835 1.000 67.7
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 756–838 1.000 67.5
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 751–833 1.000 65.9
trnC-GCA-petN_p1 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGCCCAAGCGAGACTTACTA 1005–1047 1.000 79.8
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1041–1083 1.000 78.4
trnC-GCA-petN_p3 trnC-GCA-petN CTGCAAATCCTTTTTCCCCG AGCCCAAGCGAGACTTACTA 1035–1077 1.000 78.3
trnC-GCA-petN_p4 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGAGTCCACTTCTTCCCCAT 1066–1108 1.000 78.1
trnC-GCA-petN_p5 trnC-GCA-petN TCCTTTTTCCCCGGTTCAAA AGCCCAAGCGAGACTTACTA 1028–1070 1.000 77.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 774–792 1.000 79.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 753–771 1.000 79.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 753–771 1.000 79.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 732–750 1.000 79.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 750–768 1.000 79.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GAAACGGTCCCTACGTAACC 1746–1749 1.000 82.3
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GAAACGGTCCCTACGTAACC 1749–1752 1.000 82.2
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG AAGCAATAGACCGGACCAAC 1776–1779 1.000 81.4
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA AAGCAATAGACCGGACCAAC 1779–1782 1.000 81.3
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GAAACGGTCCCTACGTAACC 1723–1726 1.000 80.6

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
Hymenopus heteromorphus NC_024062.1 162833 View on NCBI ↗
Hymenopus macrophyllus NC_030568.1 162672 View on NCBI ↗