Markers + reference

Campanula

5 species · Campanulaceae · Asterales

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Species 5
Genome length 162–170 kb
Candidate markers 248
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 248 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnV-GAC-rpl20 LSC 2053 0.1886 1.00 75.3 yes View details
trnD-GUC-psbJ LSC 1688 0.1496 1.00 74.9 yes View details
ndhB-trnM-CAU LSC 490 0.1161 1.00 72.8 yes View details
trnM-CAU-trnL-CAA LSC 8092 0.0671 1.00 71.6 yes View details
rps12-ndhH IRb 10140 0.0658 1.00 66.7 yes View details
ndhH-rps12 IRa 10140 0.0653 1.00 70.4 yes View details
trnR-UCU-atpA LSC 113 0.0496 1.00 75.8 yes View details
psbB-trnV-GAC LSC 746 0.0559 1.00 75.2 yes View details
trnM-CAU-trnM-CAU LSC 229 0.0623 1.00 74.0 yes View details
rpl32-trnL-UAG SSC 583 0.0487 1.00 73.9 yes View details
rpl2-rps19 LSC 59 0.0475 1.00 71.4 yes View details
trnT-UGU-trnL-UAA LSC 750 0.0411 1.00 69.0 yes View details
trnV-UAC-trnM-CAU LSC 196 0.0469 1.00 68.8 yes View details
atpF-atpH LSC 421 0.0380 1.00 68.4 yes View details
trnE-UUC-trnY-GUA LSC 59 0.0508 1.00 67.2 yes View details
ccsA-ndhD SSC 273 0.0590 1.00 67.2 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TTGGGTCTGCAGCTCAAATT 799–805 1.000 85.0
trnR-UCU-atpA_p2 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG TTGGGTCTGCAGCTCAAATT 802–808 1.000 84.7
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TTGGATTTGGCGCAATTGAC 746–752 1.000 84.6
trnR-UCU-atpA_p4 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG TTGGATTTGGCGCAATTGAC 749–755 1.000 84.3
trnR-UCU-atpA_p5 trnR-UCU-atpA AAATGCTGACTTGACGTCGA TTGGGTCTGCAGCTCAAATT 830–836 1.000 83.8
atpF-atpH_p1 atpF-atpH GTACAGCTGGTTGGATCCTG GGGTCGGAACAAAGAAAGGT 1092 0.200 47.6
atpF-atpH_p2 atpF-atpH GTACAGCTGGTTGGATCCTG TGGGTCGGAACAAAGAAAGG 1093 0.200 47.6
atpF-atpH_p3 atpF-atpH AGTACAGCTGGTTGGATCCT GGGTCGGAACAAAGAAAGGT 1093 0.200 47.5
atpF-atpH_p4 atpF-atpH AGTACAGCTGGTTGGATCCT TGGGTCGGAACAAAGAAAGG 1094 0.200 47.5
atpF-atpH_p5 atpF-atpH GTACAGCTGGTTGGATCCTG ATTTCTGCCGCTTCCGTTAT 847 0.200 47.5
rpl2-rps19_p1 rpl2-rps19 TGGGTAGAGCCGGATCTAAG TCTTCAGGCTAGTACCCTCG 881–885 1.000 83.0
rpl2-rps19_p2 rpl2-rps19 TGGGTAGAGCCGGATCTAAG CTAGAAGGTGGCGAGCATTT 818 0.200 47.7
rpl2-rps19_p3 rpl2-rps19 GATGACGGAAGGGAAAGACC CTAGAAGGTGGCGAGCATTT 1257 0.200 47.6
rpl2-rps19_p4 rpl2-rps19 CCAGATGACGGAAGGGAAAG CTAGAAGGTGGCGAGCATTT 1260 0.200 47.5
rpl2-rps19_p5 rpl2-rps19 GATGACGGAAGGGAAAGACC TCTTCAGGCTAGTACCCTCG 1320 0.200 47.4
psbB-trnV-GAC_p1 psbB-trnV-GAC ACACCCATATTCCAGGACCA ACCTTGTCTATTTGGCGTCC 1868 0.600 63.3
psbB-trnV-GAC_p2 psbB-trnV-GAC TGCACCAAAACCAAAGCAAG ACCTTGTCTATTTGGCGTCC 1828 0.600 63.3
psbB-trnV-GAC_p3 psbB-trnV-GAC CCCCGCGAGAAATAAATGGA ACCTTGTCTATTTGGCGTCC 1804 0.600 63.2
psbB-trnV-GAC_p4 psbB-trnV-GAC ACACCCATATTCCAGGACCA CCCCCAAATCCGTTTACCAT 1808 0.600 63.0
psbB-trnV-GAC_p5 psbB-trnV-GAC CCAACCACCCCATGAATTGA ACCTTGTCTATTTGGCGTCC 1597 0.600 62.9
trnV-GAC-rpl20_p1 trnV-GAC-rpl20 CTTCGGGGATTCGTTCAGAG TATCCCCGGCTAATTCTCGT 2527–2808 0.800 83.4
trnV-GAC-rpl20_p2 trnV-GAC-rpl20 GATTCGTTCAGAGCAAGGGT TATCCCCGGCTAATTCTCGT 2520–2801 0.800 83.2
trnV-GAC-rpl20_p3 trnV-GAC-rpl20 TACGCAATGGGAAGGTTGAG TATCCCCGGCTAATTCTCGT 2402–2683 0.800 83.1
trnV-GAC-rpl20_p4 trnV-GAC-rpl20 TGGTTCATCATTCCAAGGGC TATCCCCGGCTAATTCTCGT 2363–2644 0.800 82.8
trnV-GAC-rpl20_p5 trnV-GAC-rpl20 GTTCATCATTCCAAGGGCCT TATCCCCGGCTAATTCTCGT 2361–2642 0.800 82.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 800–818 1.000 87.5
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GACTCGAACCGATGACCATC ACCAATTTCGCCATATCCCC 831–849 1.000 86.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 808–826 1.000 86.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GACTCGAACCGATGACCATC TAGCGTCTACCAATTTCGCC 839–857 1.000 86.3
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 814–832 1.000 85.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Campanula carpatica NC_071933.1 169341 View on NCBI ↗
Campanula pallida NC_063742.1 162272 View on NCBI ↗
Campanula punctata NC_033337.1 169341 View on NCBI ↗
Campanula takesimana NC_026203.1 169551 View on NCBI ↗
Campanula zangezura NC_057269.1 166331 View on NCBI ↗