Markers + reference

Hevea

6 species · Euphorbiaceae · Malpighiales

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Species 6
Genome length 161–161 kb
Candidate markers 275
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 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 555 0.0010 1.00 27.4 yes View details
trnR(TCT)-trnT(GGT) LSC 2470 0.0011 1.00 48.6 yes View details
ndhC-trnC(ACA) LSC 659 0.0033 1.00 49.3 yes View details
psbE-petL LSC 1363 0.0010 1.00 50.3 yes View details
rpl16-rps3 LSC 1365 0.0014 1.00 50.6 yes View details
rps19 LSC 279 0.0000 1.00 19.3 yes View details
rps12-trnV(GAC) IRb 1894 0.0010 1.00 43.5 yes View details
ndhF SSC 2232 0.0009 1.00 31.4 yes View details
ndhF-rpl32 SSC 991 0.0107 1.00 58.1 yes View details
rpl32-trnL(TAG) SSC 823 0.0019 1.00 51.0 yes View details
trnV(GAC)-rps12 IRa 1894 0.0010 1.00 43.5 yes View details
rpl20-rps12 LSC 810 0.0007 1.00 50.3 yes View details
ycf3 LSC 1908 0.0005 1.00 49.4 yes View details
atpH-atpF LSC 605 0.0018 1.00 49.0 yes View details
clpP LSC 2071 0.0004 1.00 49.0 yes View details
psaJ-rpl33 LSC 469 0.0011 0.99 48.5 yes View details
trnP(TGG)-psaJ LSC 421 0.0000 1.00 48.4 yes View details
petB-petD LSC 1021 0.0000 1.00 48.4 yes View details
psaI-ycf4 LSC 456 0.0007 1.00 47.7 yes View details
rpl22-rps19 LSC 77 0.0130 1.00 47.6 yes View details
psbM-petN LSC 1365 0.0008 1.00 47.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbM-petN_p1 psbM-petN GCGACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 1522–1526 1.000 72.3
psbM-petN_p2 psbM-petN GCGACTGCACTGTTCATTCT ATGGGGAAGAAGTGGACTCT 1461–1465 1.000 70.7
psbM-petN_p3 psbM-petN GCGACTGCACTGTTCATTCT ATAGTAAGTCTCGCTTGGGC 1523–1527 1.000 66.4
psbM-petN_p4 psbM-petN GCGACTGCACTGTTCATTCT CTCGCTTGGGCTGCTTTAAT 1514–1518 1.000 66.3
psbM-petN_p5 psbM-petN GCGACTGCACTGTTCATTCTA TAGTAAGTCTCGCTTGGGCT 1522–1526 1.000 65.8
atpH-atpF_p1 atpH-atpF CGGAGGGAAAAATACGAGGT CAGTGACCCAAGGAAACGAA 752–760 1.000 75.3
atpH-atpF_p2 atpH-atpF CGAGGCGGAGGGAAAAATAC CAGTGACCCAAGGAAACGAA 757–765 1.000 75.1
atpH-atpF_p3 atpH-atpF GAGGCGGAGGGAAAAATACG CAGTGACCCAAGGAAACGAA 756–764 1.000 75.1
atpH-atpF_p4 atpH-atpF GCGGAGGGAAAAATACGAGG CAGTGACCCAAGGAAACGAA 753–761 1.000 75.1
atpH-atpF_p5 atpH-atpF GGCGGAGGGAAAAATACGAG CAGTGACCCAAGGAAACGAA 754–762 1.000 75.1
atpF_p1 atpF AGTCTATAAGAAAAGAGGAGATCA TAATGCCTACAGTAGAAGGA 600 1.000 40.1
atpF_p2 atpF AGTCTATAAGAAAAGAGGAGATCA ATAATGCCTACAGTAGAAGGA 601 1.000 40.1
atpF_p3 atpF AGTCTATAAGAAAAGAGGAGATCA AATAATGCCTACAGTAGAAGGA 602 1.000 40.1
atpF_p4 atpF GTCTATAAGAAAAGAGGAGATCA TAATGCCTACAGTAGAAGGA 599 1.000 40.1
atpF_p5 atpF AGTCTATAAGAAAAGAGGAGATCAT TAATGCCTACAGTAGAAGGA 600 1.000 40.1
trnR(TCT)-trnT(GGT)_p1 trnR(TCT)-trnT(GGT) AGAAGACCTCTGTCCTATCCA GAACCGATGACTTACGCCTT 2561–2701 1.000 64.0
trnR(TCT)-trnT(GGT)_p2 trnR(TCT)-trnT(GGT) AGGTTTAGAAGACCTCTGTCCT GAACCGATGACTTACGCCTT 2567–2707 1.000 63.3
trnR(TCT)-trnT(GGT)_p3 trnR(TCT)-trnT(GGT) AGAAGACCTCTGTCCTATCCA TACCGCTGAGTTAAAAGGGC 2526–2666 1.000 63.2
trnR(TCT)-trnT(GGT)_p4 trnR(TCT)-trnT(GGT) AGAAGACCTCTGTCCTATCCA CCGATGACTTACGCCTTACC 2558–2698 1.000 62.8
trnR(TCT)-trnT(GGT)_p5 trnR(TCT)-trnT(GGT) AGGTTTAGAAGACCTCTGTCCT TACCGCTGAGTTAAAAGGGC 2532–2672 1.000 62.6
ycf3_p1 ycf3 TGACTGATAGGGATAACAAACA TGTGGGATCGTTTTCTCATGA 2076–2084 1.000 40.4
ycf3_p2 ycf3 TGACTGATAGGGATAACAAACAA TGTGGGATCGTTTTCTCATGA 2076–2084 1.000 40.4
ycf3_p3 ycf3 TTGACTGATAGGGATAACAAACA TGTGGGATCGTTTTCTCATGA 2077–2085 1.000 40.4
ycf3_p4 ycf3 TGACTGATAGGGATAACAAACA TTGTGGGATCGTTTTCTCATGA 2077–2085 1.000 40.4
ycf3_p5 ycf3 TGACTGATAGGGATAACAAACA TGGGATCGTTTTCTCATGAGAG 2074–2082 1.000 40.4
ndhC-trnC(ACA)_p1 ndhC-trnC(ACA) CCCTTTGCTAATCGGGGATA AGAAGGTCTACGGTTCGAGT 803–838 1.000 69.3
ndhC-trnC(ACA)_p2 ndhC-trnC(ACA) CTCCGGCCCTTTGCTAATC AGAAGGTCTACGGTTCGAGT 809–844 1.000 68.9
ndhC-trnC(ACA)_p3 ndhC-trnC(ACA) TTCTCCGGCCCTTTGCTAAT AGAAGGTCTACGGTTCGAGT 811–846 1.000 68.2
ndhC-trnC(ACA)_p4 ndhC-trnC(ACA) CCCTTTGCTAATCGGGGATAA AGAAGGTCTACGGTTCGAGT 803–838 1.000 67.2
ndhC-trnC(ACA)_p5 ndhC-trnC(ACA) CCCTTTGCTAATCGGGGATA GAAGGTCTACGGTTCGAGTC 802–837 1.000 66.5

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
Hevea benthamiana MT333859.1 161124 View on NCBI ↗
Hevea brasiliensis NC_015308.1 161191 View on NCBI ↗
Hevea camargoana MN781109.1 161291 View on NCBI ↗
Hevea nitida MT413435.1 161124 View on NCBI ↗
Hevea pauciflora NC_059798.1 161123 View on NCBI ↗
Hevea spruceana NC_059799.1 161093 View on NCBI ↗