Markers + reference

Neocinnamomum

4 species · Lauraceae · Laurales

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Species 4
Genome length 151–151 kb
Candidate markers 256
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 256 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 875 0.0029 0.99 62.0 yes View details
atpF-atpH LSC 451 0.0022 1.00 34.9 yes View details
petN-psbM LSC 1076 0.0019 1.00 60.1 yes View details
psbM-trnD-GUC LSC 989 0.0020 1.00 60.4 yes View details
atpB LSC 1497 0.0013 1.00 45.6 yes View details
petA-psbJ LSC 1145 0.0081 0.99 65.7 yes View details
psbE-petL LSC 1346 0.0042 1.00 62.5 yes View details
trnP-UGG-psaJ LSC 351 0.0028 1.00 46.0 yes View details
clpP LSC 2046 0.0012 1.00 51.6 yes View details
rpoA LSC 1020 0.0020 1.00 47.8 yes View details
ycf1 IRb 939 0.0000 1.00 25.2 yes View details
ycf1 SSC 5517 0.0012 1.00 38.8 no View details
ycf1-ndhF SSC 216 0.0357 0.93 79.6 yes View details
ndhF-rpl32 SSC 970 0.0015 0.99 61.4 yes View details
rpl32-trnL-UAG SSC 606 0.0027 1.00 57.3 yes View details
rpoC1 LSC 2781 0.0010 1.00 57.1 yes View details
ndhC-trnV-UAC LSC 1760 0.0012 1.00 56.3 yes View details
rps15-ycf1 SSC 326 0.0046 1.00 56.3 yes View details
psbA-trnK-UUU LSC 262 0.0038 1.00 55.6 yes View details
atpF LSC 1291 0.0008 1.00 55.1 yes View details
trnT-UGU-trnL-UAA LSC 559 0.0009 1.00 54.8 yes View details
rpoC2 LSC 4158 0.0007 1.00 54.3 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
psbA-trnK-UUU_p1 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA GGCTTTTGGAGGGGTCTTTT 386–388 1.000 78.2
psbA-trnK-UUU_p2 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA CCTGTGCGATCAAAAATGCA 411–413 1.000 77.6
psbA-trnK-UUU_p3 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA CCCTGTGCGATCAAAAATGC 412–414 1.000 77.5
psbA-trnK-UUU_p4 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA GCCCTGTGCGATCAAAAATG 413–415 1.000 77.5
psbA-trnK-UUU_p5 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA TGCGATCAAAAATGCAAGCA 407–409 1.000 76.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCGCGCTTTTACC 940–951 1.000 79.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TCAGAAGGAACGGAGAGAGG GAACGAATCGCGCTTTTACC 998–1009 1.000 78.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GAACGAATCGCGCTTTTACC 926–937 1.000 76.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GAACGAATCGCGCTTTTACC 921–932 1.000 75.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCGCGCTTTTAC 941–952 1.000 74.9
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA AAAAGGGGGCGAAGTGATAC 1458–1460 1.000 74.1
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA GGGGGCGAAGTGATACAAAA 1454–1456 1.000 73.7
atpF_p3 atpF ACTAATTTCGTCGGCTCGAA CAAAAACAAAAAGGGGGCGA 1466–1468 1.000 72.5
atpF_p4 atpF ACTAATTTCGTCGGCTCGAA TCAAAAACAAAAAGGGGGCG 1467–1469 1.000 72.5
atpF_p5 atpF AATTTCGTCGGCTCGAATGG AAAAGGGGGCGAAGTGATAC 1455–1457 1.000 71.3
atpF-atpH_p1 atpF-atpH AGAATCGATTACGTCTTTCA GATTTACGGACTGGTCGTGG 526–535 1.000 40.5
atpF-atpH_p2 atpF-atpH AAGAATCGATTACGTCTTTCA GATTTACGGACTGGTCGTGG 527–536 1.000 40.5
atpF-atpH_p3 atpF-atpH AGAATCGATTACGTCTTTCA CGTGGCATTAGCGCTCTTAT 511–520 1.000 40.5
atpF-atpH_p4 atpF-atpH AAGAATCGATTACGTCTTTCA CGTGGCATTAGCGCTCTTAT 512–521 1.000 40.5
atpF-atpH_p5 atpF-atpH AAAGAATCGATTACGTCTTTCA GATTTACGGACTGGTCGTGG 528–537 1.000 40.5
rpoC2_p1 rpoC2 AGCAACGTACGAATAGTCCC TGGAACCAAGACCGAAATGG 257 1.000 75.3
rpoC2_p2 rpoC2 GCAACGTACGAATAGTCCCT TGGAACCAAGACCGAAATGG 256 1.000 75.3
rpoC2_p3 rpoC2 TGATTGAATCCTCGCCTTGA TGGAACCAAGACCGAAATGG 222 1.000 71.3
rpoC2_p4 rpoC2 AAGTGATTGAATCCTCGCCT TGGAACCAAGACCGAAATGG 225 1.000 71.2
rpoC2_p5 rpoC2 AGTGATTGAATCCTCGCCTT TGGAACCAAGACCGAAATGG 224 1.000 71.2
rpoC1_p1 rpoC1 TCCAGTTGAACCGGAGAGAT TTGCTCGTTCGAGAACTACG 2943–2954 1.000 79.6
rpoC1_p2 rpoC1 TCCAGTTGAACCGGAGAGAT ACGATCTTTGGCTCTGGAAC 2926–2937 1.000 79.1
rpoC1_p3 rpoC1 CCCCCTTTACTGGATCTCGA ACGATCTTTGGCTCTGGAAC 2973–2984 1.000 77.9
rpoC1_p4 rpoC1 TTCCAGTTGAACCGGAGAGA TTGCTCGTTCGAGAACTACG 2944–2955 1.000 77.8
rpoC1_p5 rpoC1 CCAGTTGAACCGGAGAGATC TTGCTCGTTCGAGAACTACG 2942–2953 1.000 77.7

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
Neocinnamomum caudatum NC_081915.1 150873 View on NCBI ↗
Neocinnamomum caudatum var. macrocarpum OR095870.1 150955 View on NCBI ↗
Neocinnamomum fargesii NC_081914.1 150842 View on NCBI ↗
Neocinnamomum mekongense NC_039718.1 150842 View on NCBI ↗