Markers + reference

Notelaea

3 species · Oleaceae · Lamiales

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Species 3
Genome length 155–155 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GUG)-psbA LSC 445 0.0045 1.00 59.1 yes View details
atpH-atpI LSC 1069 0.0025 1.00 60.3 yes View details
petN-psbM LSC 1166 0.0046 1.00 61.7 yes View details
atpB-rbcL LSC 791 0.0118 1.00 67.3 yes View details
ycf1 IRb 1164 0.0006 1.00 46.6 no View details
ndhF SSC 2217 0.0009 1.00 44.5 yes View details
ndhF-rpl32 SSC 473 0.0028 1.00 35.7 yes View details
ccsA SSC 972 0.0021 1.00 45.7 yes View details
ycf1 SSC 5631 0.0024 1.00 54.6 yes View details
trnS(GCU)-trnG(GCC) LSC 704 0.0019 0.99 60.9 yes View details
accD-psaI LSC 701 0.0029 1.00 60.6 yes View details
atpF LSC 1263 0.0005 1.00 60.2 yes View details
trnM(CAU)-psbD LSC 1316 0.0020 1.00 60.1 yes View details
psbE-petL LSC 1181 0.0011 1.00 59.5 yes View details
ycf4 LSC 555 0.0024 1.00 59.3 yes View details
ndhC-trnM(CAU) LSC 1792 0.0011 1.00 58.9 yes View details
clpP LSC 2040 0.0007 1.00 58.1 yes View details
ndhE-ndhG SSC 201 0.0066 1.00 56.7 yes View details
rpoC1 LSC 2833 0.0002 1.00 56.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH(GUG)-psbA_p1 trnH(GUG)-psbA TTAGTTATGGGCGAACGACG CCGTGCTAACCTTGGTATGG 622–625 1.000 77.4
trnH(GUG)-psbA_p2 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 567–570 1.000 77.1
trnH(GUG)-psbA_p3 trnH(GUG)-psbA TTAGTTATGGGCGAACGACG ACCGTGCTAACCTTGGTATG 623–626 1.000 76.9
trnH(GUG)-psbA_p4 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 568–571 1.000 76.9
trnH(GUG)-psbA_p5 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 568–571 1.000 76.6
trnS(GCU)-trnG(GCC)_p1 trnS(GCU)-trnG(GCC) CAATCCGACGCTTTAGTCCA AGACCGAAAGACCCTTTAACT 804–811 1.000 61.5
trnS(GCU)-trnG(GCC)_p2 trnS(GCU)-trnG(GCC) AATCCGACGCTTTAGTCCAC AGACCGAAAGACCCTTTAACT 803–810 1.000 61.5
trnS(GCU)-trnG(GCC)_p3 trnS(GCU)-trnG(GCC) ATCAACGGAACCGGAAAGAG AGACCGAAAGACCCTTTAACT 868–875 1.000 60.7
trnS(GCU)-trnG(GCC)_p4 trnS(GCU)-trnG(GCC) CATCAACGGAACCGGAAAGA AGACCGAAAGACCCTTTAACT 869–876 1.000 59.9
trnS(GCU)-trnG(GCC)_p5 trnS(GCU)-trnG(GCC) TCATCAACGGAACCGGAAAG AGACCGAAAGACCCTTTAACT 870–877 1.000 59.9
atpF_p1 atpF GGCTCGAATGGTTACCATGA AGGCAAAGTGATACAAAAAGAACT 1392–1405 1.000 40.7
atpF_p2 atpF GGCTCGAATGGTTACCATGA GGCAAAGTGATACAAAAAGAACTC 1391–1404 1.000 40.7
atpF_p3 atpF ACTAATTTCGTCGGCTCGAA AGGCAAAGTGATACAAAAAGAACT 1404–1417 1.000 40.7
atpF_p4 atpF GGCTCGAATGGTTACCATGA AGGCAAAGTGATACAAAAAGAAC 1392–1405 1.000 40.7
atpF_p5 atpF GGCTCGAATGGTTACCATGA GGCAAAGTGATACAAAAAGAACT 1391–1404 1.000 40.7
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1203 1.000 77.4
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TCCCTGTCATGTTCCTTGGA 1288 1.000 77.1
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TCCCTGTCATGTTCCTTGGA 1292 1.000 77.0
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG TCCCTGTCATGTTCCTTGGA 1213 1.000 76.8
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1220 1.000 76.5
rpoC1_p1 rpoC1 CGGAACTATGGGCCTAGTTG TTCGATTGCTCGTTCGAGAA 2995–2997 1.000 75.4
rpoC1_p2 rpoC1 CGGAACTATGGGCCTAGTTG TTTCGATTGCTCGTTCGAGA 2996–2998 1.000 75.4
rpoC1_p3 rpoC1 ATTCCGGAACTATGGGCCTA TCGATTGCTCGTTCGAGAAT 2998–3000 1.000 74.7
rpoC1_p4 rpoC1 CGGAACTATGGGCCTAGTTG TCGATTGCTCGTTCGAGAAT 2994–2996 1.000 73.7
rpoC1_p5 rpoC1 TTCCGGAACTATGGGCCTAG TTCGATTGCTCGTTCGAGAA 2998–3000 1.000 72.7
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA GCGACTGCACTATTCATTCT 1275 1.000 64.0
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT GCGACTGCACTATTCATTCT 1273 1.000 64.0
petN-psbM_p3 petN-psbM CGTAGTGTGGGGAAGAAGTG GCGACTGCACTATTCATTCT 1272 1.000 63.4
petN-psbM_p4 petN-psbM TAGTGTGGGGAAGAAGTGGA GCGACTGCACTATTCATTCT 1270 1.000 60.8
petN-psbM_p5 petN-psbM CCTGGGCTGCTTTAATGGTA GCGACTGCACTATTCATTCT 1315 1.000 60.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Notelaea longifolia NC_042458.1 155037 View on NCBI ↗
Notelaea microcarpa NC_042459.1 155019 View on NCBI ↗
Notelaea venosa NC_042427.1 155012 View on NCBI ↗