Markers + reference

Hymenaea

2 species · Fabaceae · Fabales

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Species 2
Genome length 160–161 kb
Candidate markers 268
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 657 0.0310 0.98 78.3 yes View details
atpH-atpI LSC 1493 0.0270 0.99 75.1 yes View details
trnC-GCA-petN LSC 791 0.0273 0.97 70.3 yes View details
psbZ-trnG-GCC LSC 730 0.0149 0.92 68.3 yes View details
trnG-GCC-trnfM-CAU LSC 289 0.0638 0.81 75.7 yes View details
rps4-trnT-UGU LSC 526 0.0429 0.93 77.4 yes View details
rbcL-accD LSC 1248 0.0242 0.83 68.1 yes View details
rps11-rpl36 LSC 544 0.0495 0.97 89.2 yes View details
trnR-ACG-trnN-GUU IRb 818 0.0195 0.94 74.4 yes View details
rpl32-trnL-UAG SSC 1268 0.0201 0.98 72.3 yes View details
ndhD-psaC SSC 310 0.0613 1.00 82.9 yes View details
trnH-GUG-psbA LSC 431 0.0274 0.93 75.1 yes View details
trnN-GUU-trnR-ACG IRa 818 0.0195 0.94 74.4 yes View details
rrn4.5 IRb 104 0.0300 0.96 73.3 yes View details
rrn4.5 IRa 104 0.0300 0.96 73.3 yes View details
ndhG-ndhI SSC 487 0.0234 0.97 73.1 yes View details
ndhF-rpl32 SSC 1138 0.0172 0.92 72.4 yes View details
rpl14-rpl16 LSC 148 0.0280 0.97 71.7 yes View details
atpF-atpH LSC 816 0.0205 0.78 69.9 yes View details
psaA-ycf3 LSC 826 0.0100 0.97 67.5 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCCAT 497–502 1.000 84.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCCAT 511–516 1.000 84.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCCAT 510–515 1.000 84.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCCAT 512–517 1.000 84.6
trnH-GUG-psbA_p5 trnH-GUG-psbA TATGTTATGGGCGAACGACG CCTCTAGACCTAGCTGCCAT 559–564 1.000 84.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATGAATCAAACGAGGGACCC 770–973 1.000 79.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATGAATCAAACGAGGGACCC 769–972 1.000 79.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAGATTAGCAATCCGACGCT ATGAATCAAACGAGGGACCC 778–981 1.000 78.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATGAATCAAACGAGGGACCC 824–1027 1.000 78.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC ATGAATCAAACGAGGGACCC 772–975 1.000 76.7
atpF-atpH_p1 atpF-atpH TTAAACCCGAAACTCCCAGC AGGCAGAGGGAAAAATACGG 893–1000 1.000 80.9
atpF-atpH_p2 atpF-atpH CGTATGGCCAGTAACCCAAA AGGCAGAGGGAAAAATACGG 874–981 1.000 80.8
atpF-atpH_p3 atpF-atpH TTAAACCCGAAACTCCCAGC CCTGAGGCAGAGGGAAAAAT 897–1004 1.000 80.1
atpF-atpH_p4 atpF-atpH CGTATGGCCAGTAACCCAAA CCTGAGGCAGAGGGAAAAAT 878–985 1.000 80.0
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTCCCAGC GCAGAGGGAAAAATACGGGG 891–998 1.000 79.4
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1614–1799 1.000 81.2
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1580–1765 1.000 81.2
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TCCCTGTCATGTTCCTTGGA 1663–1848 1.000 80.1
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCCTGTCATGTTCCTTGGA 1629–1814 1.000 80.1
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1581–1766 1.000 80.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 847–872 1.000 82.0
trnC-GCA-petN_p2 trnC-GCA-petN TTTATCGTTTTGGCGGCATG AGCCCAAGCGAGACTTACTA 900–925 1.000 80.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 865–890 1.000 79.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACCAGGG 898–923 1.000 79.1
trnC-GCA-petN_p5 trnC-GCA-petN TTTATCGTTTTGGCGGCATG TCTTCCCCATACTACCAGGG 951–976 1.000 77.4
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG CGTCTTCTCCTTGGCAAAGA 883–884 1.000 83.4
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 886–887 1.000 81.9
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TCCTGATGGTTGGTCGAGTA CGTCTTCTCCTTGGCAAAGA 879–880 1.000 81.7
psbZ-trnG-GCC_p4 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG GGATAGCGGGAATTGAACCC 904–905 1.000 81.6
psbZ-trnG-GCC_p5 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 884–885 1.000 81.5

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
Hymenaea courbaril NC_066083.1 160147 View on NCBI ↗
Hymenaea verrucosa NC_047323.1 160720 View on NCBI ↗