Markers + reference

Calophyllum

3 species · Calophyllaceae · Malpighiales

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Species 3
Genome length 161–161 kb
Candidate markers 269
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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 410 0.0083 0.99 47.7 yes View details
rps16 LSC 1186 0.0121 1.00 53.0 yes View details
trnS-GCU-trnG-UCC LSC 1857 0.0077 0.98 52.8 yes View details
trnG-UCC-trnR-UCU LSC 676 0.0134 0.96 68.5 yes View details
atpF-atpH LSC 553 0.0109 0.99 68.0 yes View details
atpH-atpI LSC 1157 0.0072 1.00 64.1 yes View details
rpoB-trnC-GCA LSC 1254 0.0099 1.00 63.0 yes View details
psbZ-trnG-GCC LSC 884 0.0093 0.97 61.2 yes View details
ycf4-cemA LSC 1000 0.0120 1.00 56.8 yes View details
psaJ-rpl33 LSC 529 0.0202 1.00 61.3 yes View details
ndhF SSC 2244 0.0030 1.00 44.2 yes View details
ndhF-rpl32 SSC 972 0.0113 1.00 69.1 yes View details
psbC-trnS-UGA LSC 229 0.0233 1.00 67.3 yes View details
petA-psbJ LSC 1225 0.0051 0.95 66.4 yes View details
trnL-UAA-trnF-GAA LSC 413 0.0081 1.00 64.7 yes View details
trnR-CCG-trnN-GUU IRb 633 0.0079 1.00 63.7 yes View details
trnN-GUU-trnR-ACG IRa 633 0.0079 1.00 63.7 yes View details
ndhC-trnV-UAC LSC 1258 0.0056 0.99 63.6 yes View details
accD-psaI LSC 610 0.0077 0.99 63.6 yes View details
psaA-ycf3 LSC 755 0.0035 1.00 61.5 yes View details
psbM-trnD-GUC LSC 1062 0.0063 1.00 60.9 yes View details
rpl2-trnH-GUG IRa 256 0.0208 1.00 60.7 no 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 469–479 1.000 81.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 852–862 1.000 80.1
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 851–861 1.000 80.1
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGCATGGTTCCTTGGTAACC 843–853 1.000 79.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TAGCTGCTTGGCCTGTAGTA 660–670 1.000 79.8
rps16_p1 rps16 CCTTTCAGGATCAGTCGTGG TCAAGCGGAGTTTTGCTCAT 2523–2554 1.000 80.7
rps16_p2 rps16 CCTTTCAGGATCAGTCGTGG ACCGGTTCCAAATTCAACGA 1943 0.333 53.0
rps16_p3 rps16 TCAGGATCAGTCGTGGTCTT ACCGGTTCCAAATTCAACGA 1939 0.333 52.5
rps16_p4 rps16 TTCAGGATCAGTCGTGGTCT ACCGGTTCCAAATTCAACGA 1940 0.333 52.5
rps16_p5 rps16 GCGTAAAAGATGTTAGCCGC ACCGGTTCCAAATTCAACGA 1874 0.333 52.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC CATCGTTAGCTTGGAAGGCT 1944–1983 1.000 78.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC CGTTAGCTTGGAAGGCTAGG 1941–1980 1.000 78.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TTGCTTTCATTCGGCTCCTT 1859–1898 1.000 78.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TTTGCTTTCATTCGGCTCCT 1860–1899 1.000 78.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GTTAGCTTGGAAGGCTAGGG 1940–1979 1.000 76.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTTTGTCCTATCCA 713–756 1.000 58.7
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTTTGTCCT 719–762 1.000 58.4
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTTTGTCCTATCCA 716–759 1.000 58.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTTTGTCCT 722–765 1.000 58.2
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTTTGTCCTATCCA 717–760 1.000 56.2
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA CGGAGGGAAAAATACGAGGG 696–707 1.000 82.3
atpF-atpH_p2 atpF-atpH TTAAATCCGAAACTCCCGGC CGGAGGGAAAAATACGAGGG 723–734 1.000 80.4
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA TGAGGCGGAGGGAAAAATAC 701–712 1.000 79.3
atpF-atpH_p4 atpF-atpH TTAAATCCGAAACTCCCGGC TGAGGCGGAGGGAAAAATAC 728–739 1.000 77.5
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA GCGGAGGGAAAAATACGAGG 697–708 1.000 77.0
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA CGAATCCATGGAGGGACATC 1205–1221 1.000 79.1
atpH-atpI_p2 atpH-atpI ACGGAAGCAGCAGAAATCAA CGAATCCATGGAGGGACATC 1204–1220 1.000 79.1
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA CGAATCCATGGAGGGACATC 1245–1261 1.000 78.9
atpH-atpI_p4 atpH-atpI CCTTCTACAGCTTGACCTGC CGAATCCATGGAGGGACATC 1288–1304 1.000 77.7
atpH-atpI_p5 atpH-atpI ACGGAAGCAGCAGAAATCAA GCTGCTGCTTATATAGGCGA 1221–1237 1.000 77.6

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
Calophyllum inophyllum NC_067766.1 161169 View on NCBI ↗
Calophyllum membranaceum PQ463636.1 160820 View on NCBI ↗
Calophyllum soulattri NC_068749.1 161381 View on NCBI ↗