Markers + reference

Ceropegia

4 species · Apocynaceae · Gentianales

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Species 4
Genome length 161–161 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 324 0.0243 1.00 67.5 yes View details
trnS-GCU-trnG-UCC LSC 503 0.0129 1.00 63.1 yes View details
psbM-trnD-GUC LSC 601 0.0491 1.00 71.8 yes View details
trnE-UUC-trnT-GGU LSC 956 0.0115 1.00 48.3 yes View details
psaA-ycf3 LSC 1038 0.0130 0.99 58.1 yes View details
ndhC-trnV-UAC LSC 1339 0.0138 1.00 59.8 yes View details
ndhF SSC 2244 0.0078 1.00 40.9 yes View details
rpl32-trnL-UAG SSC 910 0.0132 0.96 61.1 yes View details
ndhG-ndhI SSC 541 0.0142 1.00 47.5 yes View details
ndhA SSC 2203 0.0072 1.00 38.8 yes View details
rpl2-trnH-GUG IRa 63 0.0238 1.00 73.1 no View details
atpB-rbcL LSC 748 0.0049 1.00 62.7 yes View details
psbE-petL LSC 1137 0.0072 1.00 61.3 yes View details
rpoC1 LSC 2826 0.0021 1.00 58.1 yes View details
rpl20-rps12 LSC 872 0.0023 1.00 56.1 yes View details
rpoC2 LSC 4107 0.0026 1.00 55.7 yes View details
ycf1 IRb 5958 0.0011 0.99 55.3 yes View details
ndhD-psaC SSC 118 0.0212 1.00 53.3 yes View details
psaI-ycf4 LSC 437 0.0023 1.00 53.2 yes View details
rpoB-trnC-GCA LSC 1288 0.0080 1.00 51.8 yes View details
ycf1 IRa 5958 0.0011 1.00 46.0 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 100 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 332–393 1.000 85.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 346–407 1.000 85.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 345–406 1.000 85.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 347–408 1.000 85.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 381–442 1.000 83.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TGCAAATAAAGTTTTTGGTCGGA 624–657 1.000 59.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 550–583 1.000 57.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TGCAAATAAAGTTTTTGGTCGGA 610–643 1.000 56.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TGCAAATAAAGTTTTTGGTCGG 624–657 1.000 56.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TGCAAATAAAGTTTTTGGTCGGA 605–638 1.000 55.4
rpoC2_p1 rpoC2 AGCAGGGAAAAGTGTTGCTA CATAGCGGCGTTTTGATACC 183 1.000 70.7
rpoC2_p2 rpoC2 AGCAGGGAAAAGTGTTGCTA CCATAGCGGCGTTTTGATAC 184 1.000 70.7
rpoC2_p3 rpoC2 TGCAACATATCAGCAGGGAA CATAGCGGCGTTTTGATACC 194 1.000 69.5
rpoC2_p4 rpoC2 TGCAACATATCAGCAGGGAA CCATAGCGGCGTTTTGATAC 195 1.000 69.5
rpoC2_p5 rpoC2 CAGCAGGGAAAAGTGTTGCT CATAGCGGCGTTTTGATACC 184 1.000 68.3
rpoC1_p1 rpoC1 ACTATAATCCCGGAGAGGCC GAAGGAATAGCAGGGAAGGC 2897–2911 1.000 80.0
rpoC1_p2 rpoC1 TTTCTTGACTCGATTCGCGT GAAGGAATAGCAGGGAAGGC 2929–2943 1.000 80.0
rpoC1_p3 rpoC1 TATAATCCCGGAGAGGCCTG GAAGGAATAGCAGGGAAGGC 2895–2909 1.000 80.0
rpoC1_p4 rpoC1 ACTATAATCCCGGAGAGGCC AGCAGGGAAGGCTTAGAAGA 2889–2903 1.000 79.9
rpoC1_p5 rpoC1 TTTCTTGACTCGATTCGCGT AGCAGGGAAGGCTTAGAAGA 2921–2935 1.000 79.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCTCATTTGCATCCCC CCGGATTTGAACTGGGGAAA 1342–1423 1.000 82.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GCAAACCCCGATCAATGAAC CCGGATTTGAACTGGGGAAA 1410–1491 1.000 80.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTGCATCCCC AAAAGGATTTGCAGTCCCCC 1324–1405 1.000 80.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GCAAACCCCGATCAATGAAC AAAAGGATTTGCAGTCCCCC 1392–1473 1.000 78.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCTCATTTGCATCCCC TTTGTTGATCAGGCGACACC 1361–1442 1.000 76.8
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGCGGTAGGAACTAGAACG TTCAATTGGTCAGAGCACCG 744–789 1.000 76.4
psbM-trnD-GUC_p2 psbM-trnD-GUC GGCGGTAGGAACTAGAACGA TTCAATTGGTCAGAGCACCG 743–788 1.000 76.4
psbM-trnD-GUC_p3 psbM-trnD-GUC GCGGTAGGAACTAGAACGAA TTCAATTGGTCAGAGCACCG 742–787 1.000 76.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAAAGGCGGTAGGAACTAGA TTCAATTGGTCAGAGCACCG 748–793 1.000 74.8
psbM-trnD-GUC_p5 psbM-trnD-GUC AGTAGAAAGGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 751–796 1.000 74.1

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
Ceropegia dolichophylla NC_079600.1 161201 View on NCBI ↗
Ceropegia longifolia NC_079605.1 161223 View on NCBI ↗
Ceropegia nilotica NC_079603.1 160961 View on NCBI ↗
Ceropegia sunhangiana OR260539.1 161376 View on NCBI ↗