Markers + reference

Cyclocodon

2 species · Campanulaceae · Asterales

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Species 2
Genome length 165–167 kb
Candidate markers 269
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 534 0.0282 1.00 60.5 yes View details
rps16-trnQ-UUG LSC 1953 0.0159 1.00 52.8 yes View details
trnQ-UUG-psbK LSC 550 0.0389 0.98 67.3 yes View details
trnC-GCA-trnM-CAU LSC 1708 0.0462 0.98 75.0 yes View details
rps12-trnQ-UUG LSC 2428 0.0140 1.00 50.7 yes View details
rps3 LSC 657 0.0259 1.00 58.6 yes View details
ycf1 IRb 6876 0.0096 1.00 43.8 no View details
trnL-UAG-rpl32 SSC 849 0.0271 1.00 66.7 yes View details
ycf1 IRa 6876 0.0107 1.00 44.4 yes View details
trnG-GCC-trnfM-CAU LSC 175 0.0400 1.00 75.5 yes View details
rpoB-rpoC1 LSC 29 0.0345 1.00 72.3 yes View details
trnQ-UUG LSC 72 0.0694 1.00 68.7 yes View details
trnQ-UUG LSC 72 0.0694 1.00 68.7 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0339 1.00 66.7 yes View details
trnT-GGU-psbD LSC 1104 0.0136 1.00 66.6 yes View details
atpH-trnD-GUC LSC 1036 0.0126 1.00 66.1 yes View details
trnV-UAC-ndhC LSC 866 0.0104 1.00 64.7 yes View details
petA-psbJ LSC 998 0.0081 0.99 64.6 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCTTGAAAGGGGTGCTCAG 677–678 1.000 78.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCTTGAAAGGGGTGCTCAG 676–677 1.000 78.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGAGTCTAGTTCAGCGTCAC 1177–1178 1.000 78.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGAGTCTAGTTCAGCGTCAC 1176–1177 1.000 78.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC GGAGTCTAGTTCAGCGTCAC 1262–1263 1.000 77.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGACTTGTGTTGGATTGGCA GGGTTTTGATCCCGGCATAT 2410 0.500 59.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACTTGTGTTGGATTGGCACT GGGTTTTGATCCCGGCATAT 2408 0.500 59.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGACTTGTGTTGGATTGGCA AGATATTGGCGAGCTGTTGG 2612 0.500 59.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACTTGTGTTGGATTGGCACT AGATATTGGCGAGCTGTTGG 2610 0.500 59.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGACTTGTGTTGGATTGGCA TTGGCAAACGGACGTTTTTC 2596 0.500 58.8
trnQ-UUG_p1 trnQ-UUG TTAGTCCAACCAAGCCAACC CGAAAACTTACAGCGGCTTG 1351–1354 1.000 82.7
trnQ-UUG_p2 trnQ-UUG TTAGTCCAACCAAGCCAACC ATCGAAAACTTACAGCGGCT 1353–1356 1.000 82.3
trnQ-UUG_p3 trnQ-UUG GTCCAACCAAGCCAACCATA CGAAAACTTACAGCGGCTTG 1348–1351 1.000 82.1
trnQ-UUG_p4 trnQ-UUG TTAGTCCAACCAAGCCAACC TCGAAAACTTACAGCGGCTT 1352–1355 1.000 82.1
trnQ-UUG_p5 trnQ-UUG TTAGTCCAACCAAGCCAACC GGGCAATTTGGCGAAGAAAA 1250–1253 1.000 82.1
trnQ-UUG-psbK_p1 trnQ-UUG-psbK ATATGCCGGGATCAAAACCC CGAAAACTTACAGCGGCTTG 776–779 1.000 83.4
trnQ-UUG-psbK_p2 trnQ-UUG-psbK TTAGTCCAACCAAGCCAACC CGAAAACTTACAGCGGCTTG 1351–1354 1.000 82.7
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ATATGCCGGGATCAAAACCC CTTCACGTCCAGGATTACGG 1336–1339 1.000 82.0
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ATATGCCGGGATCAAAACCC AAAAGGAAAAGGGCCGGAAT 958 0.500 59.8
trnQ-UUG-psbK_p5 trnQ-UUG-psbK TTAGTCCAACCAAGCCAACC AAAAGGAAAAGGGCCGGAAT 1533 0.500 59.7
atpH-trnD-GUC_p1 atpH-trnD-GUC ATAACGGAAGCGGCAGAAAT TTCAATTGGTCAGAGCACCG 1131–1132 1.000 76.9
atpH-trnD-GUC_p2 atpH-trnD-GUC AGCCAATCCAGCAGCAATAA TTCAATTGGTCAGAGCACCG 1147–1148 1.000 76.0
atpH-trnD-GUC_p3 atpH-trnD-GUC AATAACGGAAGCGGCAGAAA TTCAATTGGTCAGAGCACCG 1132–1133 1.000 75.7
atpH-trnD-GUC_p4 atpH-trnD-GUC GCCAATCCAGCAGCAATAAC TTCAATTGGTCAGAGCACCG 1146–1147 1.000 75.4
atpH-trnD-GUC_p5 atpH-trnD-GUC TCCAGCAGCAATAACGGAAG TTCAATTGGTCAGAGCACCG 1141–1142 1.000 75.1
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CCAGCGTAGACATATTGCCA AAGTATGCCCCCATCGTCTA 202 1.000 78.1
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACCAGCGTAGACATATTGCC AAGTATGCCCCCATCGTCTA 203 1.000 78.1
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CCAGCGTAGACATATTGCCA TCTCTTTCAAGGAGGCAACG 167 1.000 77.7
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC ACCAGCGTAGACATATTGCC TCTCTTTCAAGGAGGCAACG 168 1.000 77.7
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC AAGTATGCCCCCATCGTCTA 181 1.000 77.3

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
Cyclocodon axillaris NC_063741.1 165444 View on NCBI ↗
Cyclocodon parviflorus MT074353.1 166588 View on NCBI ↗