Markers + reference

Calendula

2 species · Asteraceae · Asterales

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Species 2
Genome length 150–151 kb
Candidate markers 267
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnV-UAC-ndhC LSC 989 0.0051 0.99 62.2 yes View details
trnL-UAA-trnT-UGU LSC 530 0.0076 0.99 62.4 yes View details
atpH-atpI LSC 1028 0.0049 1.00 61.5 yes View details
trnD-GUC-psbM LSC 630 0.0063 1.00 62.4 yes View details
rpl32-trnL-UAG SSC 685 0.0058 1.00 57.5 yes View details
ndhD SSC 1383 0.0022 1.00 57.4 yes View details
rps15-trnN-GUU SSC 5719 0.0054 1.00 55.7 yes View details
petG-petL LSC 165 0.0182 1.00 63.0 yes View details
trnQ-UUG-rps16 LSC 849 0.0036 0.98 62.9 yes View details
psbJ-petA LSC 784 0.0051 0.99 62.6 yes View details
trnT-GGU-trnG-UCC LSC 171 0.0120 0.97 62.2 yes View details
ndhJ-trnF-GAA LSC 674 0.0057 0.78 62.0 yes View details
rps12-rpl20 LSC 733 0.0055 1.00 61.9 yes View details
rbcL-atpB LSC 735 0.0041 1.00 61.2 yes View details
psbA-trnH-GUG LSC 405 0.0076 0.98 61.2 yes View details
rpoB-trnE-UUC LSC 927 0.0022 0.99 60.7 yes View details
ycf15-rps12 IRa 945 0.0032 1.00 60.6 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
rps12-rpl20_p1 rps12-rpl20 CAGCGTCGAGGAACATGTAC TCTCCGAGCGATATATCCCC 799 1.000 74.1
rps12-rpl20_p2 rps12-rpl20 AGCGTCGAGGAACATGTACT TCTCCGAGCGATATATCCCC 798 1.000 73.4
rps12-rpl20_p3 rps12-rpl20 TCAGCGTCGAGGAACATGTA TCTCCGAGCGATATATCCCC 800 1.000 73.3
rps12-rpl20_p4 rps12-rpl20 GCGTCGAGGAACATGTACTA TCTCCGAGCGATATATCCCC 797 1.000 73.3
rps12-rpl20_p5 rps12-rpl20 CAGCGTCGAGGAACATGTAC TTCTACGTCTCCGAGCGATA 806 1.000 72.7
petG-petL_p1 petG-petL TCAAAGGTCCAACTGATCGC TAGCTCCTTGATGCCTACCA 385 1.000 77.7
petG-petL_p2 petG-petL TCAAAGGTCCAACTGATCGC AGCTCCTTGATGCCTACCAT 384 1.000 75.2
petG-petL_p3 petG-petL CGCCACGCCTGTATTGTAAA TAGCTCCTTGATGCCTACCA 368 1.000 71.9
petG-petL_p4 petG-petL TCAAAGGTCCAACTGATCGC TGGTCTGAGCAAGATACGAC 307 1.000 71.7
petG-petL_p5 petG-petL TCAAAGGTCCAACTGATCGC AGCTCCTTGATGCCTACCA 384 1.000 71.0
psbJ-petA_p1 psbJ-petA TGTGATCGGTTTAGTAGGCG ACGTGTACAAGGCCTTTTGT 953–960 1.000 76.0
psbJ-petA_p2 psbJ-petA GTGATCGGTTTAGTAGGCGT ACGTGTACAAGGCCTTTTGT 952–959 1.000 76.0
psbJ-petA_p3 psbJ-petA TGTGATCGGTTTAGTAGGCG GGCCTTTTGTTCTTCTTCGC 943–950 1.000 75.9
psbJ-petA_p4 psbJ-petA GTGATCGGTTTAGTAGGCGT GGCCTTTTGTTCTTCTTCGC 942–949 1.000 75.9
psbJ-petA_p5 psbJ-petA TATTCCGGATTGGGTTCGTC ACGTGTACAAGGCCTTTTGT 916–923 1.000 75.7
rbcL-atpB_p1 rbcL-atpB CACCAGCTTTGAATCCAACAC CTACATCTAGTACCGGCCCA 877–878 1.000 72.2
rbcL-atpB_p2 rbcL-atpB ACCAGCTTTGAATCCAACACT CTACATCTAGTACCGGCCCA 876–877 1.000 71.9
rbcL-atpB_p3 rbcL-atpB CACCAGCTTTGAATCCAACAC ATCTAGTACCGGCCCAATGA 873–874 1.000 71.5
rbcL-atpB_p4 rbcL-atpB CACCAGCTTTGAATCCAACAC TCTAGTACCGGCCCAATGAT 872–873 1.000 71.5
rbcL-atpB_p5 rbcL-atpB CACCAGCTTTGAATCCAACAC GATACGCCCCAGGTTCTTTT 846–847 1.000 71.2
trnV-UAC-ndhC_p1 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT GTCCTTTGCTAATCGGAGCT 1134–1154 1.000 76.6
trnV-UAC-ndhC_p2 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT CGGTCCTTTGCTAATCGGAG 1136–1156 1.000 75.7
trnV-UAC-ndhC_p3 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT CTCCGGTCCTTTGCTAATCG 1139–1159 1.000 75.7
trnV-UAC-ndhC_p4 trnV-UAC-ndhC GAAGGTCTACGGTTCGAGTC GTCCTTTGCTAATCGGAGCT 1133–1153 1.000 73.8
trnV-UAC-ndhC_p5 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT GGTCCTTTGCTAATCGGAGC 1135–1155 1.000 73.5
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA AGTTGGATAGGATGGCCCTT GTGCAGAGACTCGATGGAAG 1306–1452 1.000 82.9
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA ACAAGTTTCAGGTTGGGCAT GTGCAGAGACTCGATGGAAG 1961–2107 1.000 82.8
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA GAAAAAGTCGCGGCTCAATC GTGCAGAGACTCGATGGAAG 1792–1938 1.000 82.6
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA TGGCATTCCATTGCTGTCAT GTGCAGAGACTCGATGGAAG 1606–1752 1.000 82.4
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA ACAAGTTTCAGGTTGGGCAT AGAGACTCGATGGAAGCTGT 1957–2103 1.000 82.2

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
Calendula arvensis NC_066014.1 150682 View on NCBI ↗
Calendula officinalis NC_066028.1 150465 View on NCBI ↗