Markers + reference

Hopea

4 species · Dipterocarpaceae · Malvales

Back to catalogue

Species 4
Genome length 151–152 kb
Candidate markers 260
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2244 0.2391 0.82 78.3 yes View details
ndhD SSC 1503 0.2859 0.87 81.3 yes View details
psaC SSC 246 0.2940 0.83 74.1 yes View details
ndhE SSC 306 0.2778 0.88 75.5 yes View details
ndhG SSC 531 0.3032 0.96 81.9 yes View details
ndhG-ndhI SSC 305 0.3224 0.99 74.0 yes View details
ndhI SSC 504 0.3145 0.93 80.9 yes View details
ndhA SSC 2164 0.2597 0.83 78.8 yes View details
ndhH SSC 1182 0.2745 0.83 80.1 yes View details
rps15-trnN-GUU SSC 6411 0.2438 0.82 73.5 yes View details
rpl32-trnL-UAG SSC 1340 0.2550 0.84 80.5 yes View details
ndhF-rpl32 SSC 712 0.2457 0.81 79.3 yes View details
ccsA SSC 966 0.2424 0.78 78.7 yes View details
rpl2-trnH-GUG IRa 132 0.0732 1.00 75.3 no View details
rps15 SSC 273 0.2497 0.75 71.7 yes View details
psbZ-trnG-UCC LSC 621 0.0115 1.00 71.3 yes View details
ccsA-ndhD SSC 252 0.2136 0.73 71.1 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbZ-trnG-UCC_p1 psbZ-trnG-UCC CTTCTCCTGATGGTTGGGTG CGTCTTCTCCTTGGCAAAGA 775–851 1.000 81.8
psbZ-trnG-UCC_p2 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 778–854 1.000 81.1
psbZ-trnG-UCC_p3 psbZ-trnG-UCC TTCTCCTGATGGTTGGGTGA CGTCTTCTCCTTGGCAAAGA 774–850 1.000 80.7
psbZ-trnG-UCC_p4 psbZ-trnG-UCC CTTCTCCTGATGGTTGGGTG TAAATACATTGCCTGGGCGG 814–890 1.000 80.4
psbZ-trnG-UCC_p5 psbZ-trnG-UCC TCCTGATGGTTGGGTGAGTA CGTCTTCTCCTTGGCAAAGA 771–847 1.000 80.1
ndhF_p1 ndhF ACCCCCGTAACTTCTTCGTA ATTGTTGTCGCAGTCCACTT 2830–2850 0.500 60.3
ndhF_p2 ndhF TCGTAACCCCCGTAACTTCT ATTGTTGTCGCAGTCCACTT 2835–2855 0.500 60.3
ndhF_p3 ndhF CAATTCCCGTTCTCAACCCA ATTGTTGTCGCAGTCCACTT 2881–2901 0.500 60.1
ndhF_p4 ndhF GAGGTTTCCTTCGTAACCCC ATTGTTGTCGCAGTCCACTT 2845–2865 0.500 60.0
ndhF_p5 ndhF ATTCCCGTTCTCAACCCATG ATTGTTGTCGCAGTCCACTT 2879–2899 0.500 59.8
ndhF-rpl32_p1 ndhF-rpl32 AAAAGCCCACATACGACGAA AAAAAGAATCCCCATCCCGG 1160–1200 0.500 60.7
ndhF-rpl32_p2 ndhF-rpl32 AAAGCCCACATACGACGAAA AAAAAGAATCCCCATCCCGG 1159–1199 0.500 60.7
ndhF-rpl32_p3 ndhF-rpl32 AAGCCCACATACGACGAAAA AAAAAGAATCCCCATCCCGG 1158–1198 0.500 60.7
ndhF-rpl32_p4 ndhF-rpl32 AAGCCCACATACGACGAAAA CAAAGCTTTCAACGCTGTCC 901–932 0.500 59.9
ndhF-rpl32_p5 ndhF-rpl32 GGTCGTGTGAACCAAAAACC AAAAAGAATCCCCATCCCGG 1540–1580 0.500 59.7
rpl32-trnL-UAG_p1 rpl32-trnL-UAG AAGTGGACTGCGACAACAAT AAAAGGCCCGAAGTAGCAAA 2355–2382 0.500 61.6
rpl32-trnL-UAG_p2 rpl32-trnL-UAG AAGTGGACTGCGACAACAAT GCTGGTACTAATGTTGCGGA 2391–2418 0.500 61.6
rpl32-trnL-UAG_p3 rpl32-trnL-UAG AAGTGGACTGCGACAACAAT AGCTGGTACTAATGTTGCGG 2392–2419 0.500 61.5
rpl32-trnL-UAG_p4 rpl32-trnL-UAG AAGTGGACTGCGACAACAAT AACCATCGGGATTGAAGAGC 2409–2436 0.500 61.4
rpl32-trnL-UAG_p5 rpl32-trnL-UAG AAGTGGACTGCGACAACAAT CGGGATTGAAGAGCTGGTAC 2403–2430 0.500 61.3
ccsA_p1 ccsA TGGAATTGGTAGACACGCTG ACTATCAGGTGAGAGGGTCG 1459 0.500 59.4
ccsA_p2 ccsA GTGGAATTGGTAGACACGCT ACTATCAGGTGAGAGGGTCG 1460 0.500 59.4
ccsA_p3 ccsA TAGACACGCTGCTCTTAGGA ACTATCAGGTGAGAGGGTCG 1450 0.500 59.2
ccsA_p4 ccsA TGGAATTGGTAGACACGCTG CGGCTTGTTTATCTCGACGA 1842 0.500 59.1
ccsA_p5 ccsA GTGGAATTGGTAGACACGCT CGGCTTGTTTATCTCGACGA 1843 0.500 59.0
ccsA-ndhD_p1 ccsA-ndhD TTTGCTACTTCGGGCCTTTT CTCTTTTCCCCTTGGTTGCT 1566 0.500 60.5
ccsA-ndhD_p2 ccsA-ndhD TTTGCTACTTCGGGCCTTTT TCTCTTTTCCCCTTGGTTGC 1567 0.500 60.4
ccsA-ndhD_p3 ccsA-ndhD TCCGCAACATTAGTACCAGC CTCTTTTCCCCTTGGTTGCT 1530 0.500 60.4
ccsA-ndhD_p4 ccsA-ndhD TCCGCAACATTAGTACCAGC TCTCTTTTCCCCTTGGTTGC 1531 0.500 60.4
ccsA-ndhD_p5 ccsA-ndhD CCGCAACATTAGTACCAGCT CTCTTTTCCCCTTGGTTGCT 1529 0.500 60.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Hopea chinensis NC_053766.1 151454 View on NCBI ↗
Hopea dryobalanoides MH791329.1 150943 View on NCBI ↗
Hopea hainanensis NC_044642.1 151795 View on NCBI ↗
Hopea mollissima MZ160993.1 151497 View on NCBI ↗