Markers + reference

Anthoshorea

2 species · Dipterocarpaceae · Malvales

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Species 2
Genome length 152–152 kb
Candidate markers 242
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 242 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0028 1.00 48.9 yes View details
rps16-trnQ-UUG LSC 1571 0.0311 0.98 67.0 yes View details
trnS-GCU-trnR-UCU LSC 1576 0.0217 0.99 64.0 yes View details
atpF LSC 555 0.0072 1.00 47.7 yes View details
psbZ-trnG-UCC LSC 609 0.0399 0.95 82.5 yes View details
trnT-UGU-trnL-UAA LSC 990 0.0245 0.83 66.7 yes View details
clpP LSC 1422 0.0255 0.99 59.8 yes View details
rps15-trnN-GUU SSC 6446 0.0192 0.94 54.1 yes View details
trnH-GUG-psbA LSC 188 0.0934 0.97 82.1 yes View details
rpl23-trnI-CAU IRb 270 0.0596 0.87 74.6 yes View details
trnfM-CAU-rps14 LSC 168 0.0314 0.95 70.6 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0339 1.00 69.0 yes View details
ndhC-trnV-UAC LSC 1012 0.0168 1.00 68.5 yes View details
petG-trnW-CCA LSC 149 0.0268 1.00 67.9 yes View details
rpl2-trnH-GUG LSC 128 0.1000 0.55 67.6 no View details
rps14-psaB LSC 129 0.0465 1.00 67.2 yes View details
petN-psbM LSC 705 0.0256 0.94 66.5 yes View details
psbN-psbH LSC 98 0.0213 0.96 65.7 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 85 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 TTCCCTCTAGACCTAGCTGC 252–258 1.000 85.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 266–272 1.000 85.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 265–271 1.000 85.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 267–273 1.000 85.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACAATCCACTGCCTT TTCCCTCTAGACCTAGCTGC 272–278 1.000 85.0
psbA_p1 psbA TGCTCCTTTATTTTCAAAAACTCGT TTGTGTACTTGGGAGTCCCT 1153 1.000 40.2
psbA_p2 psbA TGCTCCTTTATTTTCAAAAACTCG TTGTGTACTTGGGAGTCCCT 1153 1.000 40.2
psbA_p3 psbA GCTCCTTTATTTTCAAAAACTCGT TTGTGTACTTGGGAGTCCCT 1152 1.000 40.2
psbA_p4 psbA TGCTCCTTTATTTTCAAAAACTCGT ACTTGGGAGTCCCTGATGAT 1147 1.000 40.2
psbA_p5 psbA TGCTCCTTTATTTTCAAAAACTCGT GTGTACTTGGGAGTCCCTGA 1151 1.000 40.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGGTCCCGGTGATCAAAG 1661–1902 1.000 81.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CCGGTGATCAAAGGTTCGAA 1654–1895 1.000 80.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AATAGACAGAATGGGGCGTG 1703–1944 1.000 79.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTTTGGTCCCGGTGATCAA 1663–1904 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCCCGGTGATCAAAGGTTC 1657–1898 1.000 77.8
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU AGCAAAACGGAAAGAGAGGG TGTCCACTAAATTGCGTCCA 1755–1850 1.000 76.7
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU GCAAAACGGAAAGAGAGGGA TGTCCACTAAATTGCGTCCA 1754–1849 1.000 76.7
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA TGTCCACTAAATTGCGTCCA 1749–1844 1.000 76.3
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AGCAAAACGGAAAGAGAGGG GTGTCCACTAAATTGCGTCC 1756–1851 1.000 74.0
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU GCAAAACGGAAAGAGAGGGA GTGTCCACTAAATTGCGTCC 1755–1850 1.000 73.9
atpF_p1 atpF AGTAAGCCTCACTCACTGGT AAAGTATCGCGAGACAACCC 1660–1723 1.000 81.3
atpF_p2 atpF TACCTGTTTGCCTATCCCCA AAAGTATCGCGAGACAACCC 1873–1936 1.000 81.1
atpF_p3 atpF AGTAAGCCTCACTCACTGGT CCCAGGCGGATGGAAAAATA 1642–1705 1.000 80.9
atpF_p4 atpF CGGCTTTAATGGTTGCCATG AAAGTATCGCGAGACAACCC 1366–1429 1.000 80.8
atpF_p5 atpF TACCTGTTTGCCTATCCCCA CCCAGGCGGATGGAAAAATA 1855–1918 1.000 80.6
petN-psbM_p1 petN-psbM TGTCACTCGTAGTATGGGGA ATTGCTACTGCGCTGTTCAT 816–821 1.000 77.0
petN-psbM_p2 petN-psbM ACATTTTCCCTGTCACTCGT ATTGCTACTGCGCTGTTCAT 826–831 1.000 76.0
petN-psbM_p3 petN-psbM TGTCACTCGTAGTATGGGGA TATTGCTACTGCGCTGTTCA 817–822 1.000 76.0
petN-psbM_p4 petN-psbM TGTCACTCGTAGTATGGGGA TTGCTACTGCGCTGTTCATT 815–820 1.000 75.3
petN-psbM_p5 petN-psbM ACATTTTCCCTGTCACTCGT TATTGCTACTGCGCTGTTCA 827–832 1.000 75.0

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
Anthoshorea henryana MZ160995.1 151685 View on NCBI ↗
Anthoshorea roxburghii MZ160996.1 151795 View on NCBI ↗