Markers + reference

Plumeria

3 species · Apocynaceae · Gentianales

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Species 3
Genome length 154–154 kb
Candidate markers 269
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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 463 0.0106 0.95 57.8 yes View details
psbE-petL LSC 1090 0.0092 1.00 51.5 yes View details
trnP-UGG-psaJ LSC 351 0.0076 1.00 49.9 yes View details
clpP LSC 2031 0.0039 1.00 47.3 yes View details
ycf1 IRb 1071 0.0012 1.00 32.3 no View details
ndhF SSC 2229 0.0036 1.00 48.0 yes View details
rpl32-trnL-UAG SSC 971 0.0089 1.00 52.4 yes View details
ndhD SSC 1503 0.0018 1.00 46.2 yes View details
ycf1 SSC 5487 0.0051 1.00 42.6 yes View details
ndhD-psaC SSC 115 0.0754 1.00 68.5 yes View details
trnM-CAU-atpE LSC 245 0.0181 0.98 67.0 yes View details
rpl2-trnH-GUG IRa 51 0.0392 1.00 64.3 no View details
atpH-atpI LSC 1158 0.0043 1.00 64.1 yes View details
rpl2-rpl23 IRb 18 0.0370 1.00 63.6 yes View details
rpl23-rpl2 IRa 18 0.0370 1.00 63.6 yes View details
ndhC-trnV-UAC LSC 1197 0.0058 1.00 62.9 yes View details
petA-psbJ LSC 987 0.0047 1.00 62.7 yes View details
ycf4-cemA LSC 693 0.0029 0.99 62.1 yes View details
trnT-GGU-psbD LSC 1258 0.0037 1.00 61.4 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 GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 505–530 1.000 83.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 519–544 1.000 83.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 518–543 1.000 83.3
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 508–533 1.000 83.3
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 520–545 1.000 83.2
trnK-UUU_p1 trnK-UUU TGCTAGTGTCAACCAATATCGA AACAAGGGGATCGGTCTAGA 2989 1.000 54.4
trnK-UUU_p2 trnK-UUU TGCTAGTGTCAACCAATATCGA ACAAGGGGATCGGTCTAGAA 2988 1.000 54.4
trnK-UUU_p3 trnK-UUU CCAAGCGCACACATTCTCTA GCTCAATGGTTTAATTGCTTCG 2890 1.000 53.7
trnK-UUU_p4 trnK-UUU CCAAGCGCACACATTCTCTA AGCTCAATGGTTTAATTGCTTCG 2891 1.000 52.3
trnK-UUU_p5 trnK-UUU TGCTAGTGTCAACCAATATCGA GGAGATAACAAGGGGATCGG 2995 1.000 52.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1219–1247 1.000 77.7
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TTTTTGCAACTTTAGCCGCG 1302–1330 1.000 76.8
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TTTTTGCAACTTTAGCCGCG 1306–1334 1.000 76.8
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1220–1248 1.000 76.6
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT CCGCGGCTTATATAGGTGAA 1204–1232 1.000 76.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GAAACGGTCCCTACGTAACC 1414–1419 1.000 79.7
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGACCAGCCTACAAAAACGA 1432–1437 1.000 78.8
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GAAACGGTCCCTACGTAACC 1377–1382 1.000 78.3
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1422–1427 1.000 77.8
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1395–1400 1.000 77.4
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT AGAAGGTCTACGGTTCGAGT 885–1336 1.000 82.0
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CTGGTCCTTTGCTAATCGGG AGAAGGTCTACGGTTCGAGT 902–1353 1.000 80.4
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CCTTTGCTAATCGGGGCTAA AGAAGGTCTACGGTTCGAGT 897–1348 1.000 80.4
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT GAAGGTCTACGGTTCGAGTC 884–1335 1.000 79.2
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TCCTTTGCTAATCGGGGCTA AGAAGGTCTACGGTTCGAGT 898–1349 1.000 79.1
trnM-CAU-atpE_p1 trnM-CAU-atpE GGCGAGAGTCATTGGTTCAA CGGGTAGAGGCTATCAATGC 299–307 1.000 81.5
trnM-CAU-atpE_p2 trnM-CAU-atpE GGCGAGAGTCATTGGTTCAA GGGTAGAGGCTATCAATGCG 298–306 1.000 81.5
trnM-CAU-atpE_p3 trnM-CAU-atpE GGCGAGAGTCATTGGTTCAA GGTAGAGGCTATCAATGCGG 297–305 1.000 81.5
trnM-CAU-atpE_p4 trnM-CAU-atpE GGCGAGAGTCATTGGTTCAA ACACGGGTAGAGGCTATCAA 302–310 1.000 80.9
trnM-CAU-atpE_p5 trnM-CAU-atpE ATTGCTTTCATACGGCGAGA GGTAGAGGCTATCAATGCGG 310–318 1.000 80.4

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
Plumeria krugii NC_069179.1 154216 View on NCBI ↗
Plumeria obtusa NC_069180.1 154329 View on NCBI ↗
Plumeria rubra NC_046018.1 153912 View on NCBI ↗