Markers + reference

Cyanea

2 species · Campanulaceae · Asterales

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Species 2
Genome length 164–165 kb
Candidate markers 283
Primer pairs 75

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 6 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ORF243 LSC 732 0.2467 0.84 80.4 yes View details
ORF243-trnQ (UUG) LSC 336 0.4735 0.79 73.8 yes View details
trnQ (UUG)-psbK LSC 615 0.0787 0.87 79.2 yes View details
ORF310 LSC 933 0.0751 0.97 78.4 yes View details
ORF310-trnC (GCA) LSC 531 0.0852 0.84 75.9 yes View details
ndhC-ORF225 LSC 439 0.0971 0.87 76.8 yes View details
ORF225 LSC 678 0.1032 1.00 78.9 yes View details
rpl23-trnI (CAU) IRb 751 0.1062 0.51 76.1 yes View details
trnI (CAU)-rpl23 IRa 751 0.1062 0.51 76.1 yes View details
rpoC2-rpoC1 LSC 166 0.0482 1.00 80.2 yes View details
psbA-rbcL LSC 1062 0.0291 0.94 79.8 yes View details
rps16-ORF243 LSC 162 0.1060 0.93 76.8 yes View details
trnM (CAU)-trnV (UAC) LSC 197 0.0428 0.95 74.5 yes View details
rpoC1-rpoB LSC 43 0.0698 1.00 73.1 yes View details
rpl16-rps3 LSC 165 0.0494 0.98 72.0 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-rbcL_p1 psbA-rbcL TACAGAAGCGACCCCATAGG ATTTGAGTTTGCCGCAATGG 1098–1148 1.000 80.7
psbA-rbcL_p2 psbA-rbcL TACAGAAGCGACCCCATAGG GCTGCTTGTGAGGTATGGAA 1127–1177 1.000 80.4
psbA-rbcL_p3 psbA-rbcL TACAGAAGCGACCCCATAGG TGAGTTTGCCGCAATGGATA 1095–1145 1.000 80.4
psbA-rbcL_p4 psbA-rbcL TACAGAAGCGACCCCATAGG AGTTTGCCGCAATGGATACT 1093–1143 1.000 80.3
psbA-rbcL_p5 psbA-rbcL ATCCAGTTACAGAAGCGACC ATTTGAGTTTGCCGCAATGG 1105–1155 1.000 80.0
trnM (CAU)-trnV (UAC)_p1 trnM (CAU)-trnV (UAC) CCCGCCGTATGAAAGCAATA ACCAACTGAGCTATAGCCCT 251–261 1.000 80.9
trnM (CAU)-trnV (UAC)_p2 trnM (CAU)-trnV (UAC) CCCGCCGTATGAAAGCAATA TTGCATGATGGACTCCCTTG 305–315 1.000 80.3
trnM (CAU)-trnV (UAC)_p3 trnM (CAU)-trnV (UAC) CCCGCCGTATGAAAGCAATA TGATTGCATGATGGACTCCC 308–318 1.000 78.5
trnM (CAU)-trnV (UAC)_p4 trnM (CAU)-trnV (UAC) CCGCCGTATGAAAGCAATAC TTGCATGATGGACTCCCTTG 304–314 1.000 78.3
trnM (CAU)-trnV (UAC)_p5 trnM (CAU)-trnV (UAC) CCCGCCGTATGAAAGCAATA GCATGATGGACTCCCTTGAA 303–313 1.000 78.0
rps16-ORF243_p1 rps16-ORF243 AGCGAACATCAATTGCAACG AAAAAGTACGAACCGGTGCT 546–547 1.000 89.0
rps16-ORF243_p2 rps16-ORF243 AGCGAACATCAATTGCAACG GCCCTCCAAGCGAATCTAAA 370 0.500 59.4
rps16-ORF243_p3 rps16-ORF243 AGCGAACATCAATTGCAACG ACGTTGGATTTTGTCACGGA 297 0.500 59.4
rps16-ORF243_p4 rps16-ORF243 GCGAACATCAATTGCAACGA GCCCTCCAAGCGAATCTAAA 369 0.500 59.4
rps16-ORF243_p5 rps16-ORF243 TGCTTTCTACCACAGCGTTT GCCCTCCAAGCGAATCTAAA 332 0.500 59.4
ORF243_p1 ORF243 AGCGAACATCAATTGCAACG CAAAGATTGCTGCGGGAAAG 2014–2294 1.000 91.6
ORF243_p2 ORF243 GCGAACATCAATTGCAACGA CAAAGATTGCTGCGGGAAAG 2013–2293 1.000 91.6
ORF243_p3 ORF243 TGCTTTCTACCACAGCGTTT CAAAGATTGCTGCGGGAAAG 1976–2256 1.000 91.6
ORF243_p4 ORF243 TTGCTTTCTACCACAGCGTT CAAAGATTGCTGCGGGAAAG 1977–2257 1.000 91.6
ORF243_p5 ORF243 AGCGAACATCAATTGCAACG GGCAAATCGTCCCAATTTCG 1242 0.500 59.0
ORF243-trnQ (UUG)_p1 ORF243-trnQ (UUG) AGCGAACATCAATTGCAACG CAAAGATTGCTGCGGGAAAG 2014–2294 1.000 91.6
ORF243-trnQ (UUG)_p2 ORF243-trnQ (UUG) GCGAACATCAATTGCAACGA CAAAGATTGCTGCGGGAAAG 2013–2293 1.000 91.6
ORF243-trnQ (UUG)_p3 ORF243-trnQ (UUG) TGCTTTCTACCACAGCGTTT CAAAGATTGCTGCGGGAAAG 1976–2256 1.000 91.6
ORF243-trnQ (UUG)_p4 ORF243-trnQ (UUG) TTGCTTTCTACCACAGCGTT CAAAGATTGCTGCGGGAAAG 1977–2257 1.000 91.6
ORF243-trnQ (UUG)_p5 ORF243-trnQ (UUG) TTTAGATTCGCTTGGAGGGC CAAAGATTGCTGCGGGAAAG 1944 0.500 59.6
trnQ (UUG)-psbK_p1 trnQ (UUG)-psbK CTTACCACTCGGCTACGC ACAGATACAGATCAAACTTAAAAGA 604–670 1.000 49.3
trnQ (UUG)-psbK_p2 trnQ (UUG)-psbK CTTACCACTCGGCTACGC AACAGATACAGATCAAACTTAAAAGA 605–671 1.000 49.3
trnQ (UUG)-psbK_p3 trnQ (UUG)-psbK CTTACCACTCGGCTACGC ACAGATACAGATCAAACTTAAAAG 604–670 1.000 49.3
trnQ (UUG)-psbK_p4 trnQ (UUG)-psbK CGCCTTACCACTCGGCTA ACAGATACAGATCAAACTTAAAAGA 607–673 1.000 49.3
trnQ (UUG)-psbK_p5 trnQ (UUG)-psbK GCCTTACCACTCGGCTAC ACAGATACAGATCAAACTTAAAAGA 606–672 1.000 49.3

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
Cyanea fissa NC_033363.1 165068 View on NCBI ↗
Cyanea leptostegia NC_035356.1 163907 View on NCBI ↗