Markers + reference

Campsis

2 species · Bignoniaceae · Lamiales

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Species 2
Genome length 154–154 kb
Candidate markers 271
Primer pairs 80

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 7 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5481 0.3730 0.86 74.9 yes View details
ycf1-rps15 SSC 392 0.4595 0.88 77.4 yes View details
ndhA SSC 2183 0.4624 0.75 76.5 yes View details
ndhI SSC 507 0.5114 0.95 81.7 yes View details
ndhI-ndhG SSC 349 0.4803 0.87 76.2 yes View details
ndhG SSC 531 0.5169 0.67 74.2 yes View details
ndhD SSC 1521 0.4754 0.88 81.7 yes View details
ccsA SSC 978 0.4709 0.86 81.1 yes View details
ndhF SSC 2238 0.4599 0.80 77.8 yes View details
ycf1 IRa 1023 0.0060 0.98 49.2 no View details
petB-petD LSC 193 0.0688 0.98 85.4 yes View details
trnL-UAG-ndhF SSC 1577 0.4558 0.85 80.5 yes View details
ndhH SSC 1182 0.4491 0.81 79.8 yes View details
rps15 SSC 273 0.4457 0.95 77.4 yes View details
trnT-UGU-trnL-UAA LSC 737 0.0408 0.96 77.0 yes View details
ndhE-psaC SSC 250 0.4764 0.93 76.8 yes View details
ndhD-ccsA SSC 248 0.4498 0.92 76.7 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
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 797–798 1.000 82.6
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 829–830 1.000 81.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA AAAATAGGAAAAGGCCGGCT CCGTAGCGTCTACCGATTTC 852–853 1.000 81.4
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 791–792 1.000 81.3
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GGTTTCCATACCAAGGCTCA 829–830 1.000 80.3
petB-petD_p1 petB-petD GCCGCTTCTTACTGCTGTAT GTTCAAGTCACACACTCCCA 290 1.000 81.6
petB-petD_p2 petB-petD GCCGCTTCTTACTGCTGTAT GTTACACGGTGGTTGGAACA 371 1.000 80.5
petB-petD_p3 petB-petD GCCGCTTCTTACTGCTGTAT ATAGGGGTTACACGGTGGTT 377 1.000 80.4
petB-petD_p4 petB-petD GCCGCTTCTTACTGCTGTAT AGTTCAAGTCACACACTCCC 291 1.000 79.2
petB-petD_p5 petB-petD GCCGCTTCTTACTGCTGTAT TATAGGGGTTACACGGTGGT 378 1.000 78.7
ycf1_p1 ycf1 AGGAAGCACCAAACCAATCA ACATACTGAAACGACTGCCA 415 0.500 50.3
ycf1_p2 ycf1 AAGAGGAAGCACCAAACCAA ACATACTGAAACGACTGCCA 418 0.500 49.7
ycf1_p3 ycf1 CATTCGTCTGTCTGTCCCAA ACATACTGAAACGACTGCCA 488 0.500 49.7
ycf1_p4 ycf1 AACCCATTCGTCTGTCTGTC ACATACTGAAACGACTGCCA 492 0.500 49.7
ycf1_p5 ycf1 GAACCCATTCGTCTGTCTGT ACATACTGAAACGACTGCCA 493 0.500 49.7
ycf1-rps15_p1 ycf1-rps15 AGCAGCCAAGTTTCACATGA CAGCAGTCGTTGACGTTTTC 788 0.500 59.8
ycf1-rps15_p2 ycf1-rps15 AGCAGCCAAGTTTCACATGA TCCCAACGCGTTACATAAGG 1177 0.500 59.8
ycf1-rps15_p3 ycf1-rps15 AGCAGCCAAGTTTCACATGA AGTCGTTGACGTTTTCCCAA 784 0.500 59.7
ycf1-rps15_p4 ycf1-rps15 AGCAGCCAAGTTTCACATGA CCGAGTCATTCTTCCATGCA 956 0.500 59.7
ycf1-rps15_p5 ycf1-rps15 GCAGCCAAGTTTCACATGAC CAGCAGTCGTTGACGTTTTC 787 0.500 59.5
rps15_p1 rps15 AGCAGCCAAGTTTCACATGA TCCCAACGCGTTACATAAGG 1177 0.500 59.8
rps15_p2 rps15 AGCAGCCAAGTTTCACATGA CCGAGTCATTCTTCCATGCA 956 0.500 59.7
rps15_p3 rps15 GCAGCCAAGTTTCACATGAC TCCCAACGCGTTACATAAGG 1176 0.500 59.4
rps15_p4 rps15 AGCAGCCAAGTTTCACATGA AACACCATGCATTGATGGGT 1040 0.500 59.4
rps15_p5 rps15 CAGCAGCCAAGTTTCACATG TCCCAACGCGTTACATAAGG 1178 0.500 59.4
ndhH_p1 ndhH GAAAACGTCAACGACTGCTG TGAAGAATTCCCAAAGGCCC 1601 0.500 59.5
ndhH_p2 ndhH GAAAACGTCAACGACTGCTG GCTATGGAGGGACCGATACT 1694 0.500 59.4
ndhH_p3 ndhH GAAAACGTCAACGACTGCTG CTGCTATGGAGGGACCGATA 1696 0.500 59.4
ndhH_p4 ndhH TTGGGAAAACGTCAACGACT TGAAGAATTCCCAAAGGCCC 1605 0.500 59.3
ndhH_p5 ndhH TGCATGGAAGAATGACTCGG TGAAGAATTCCCAAAGGCCC 1433 0.500 59.3

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
Campsis grandiflora NC_061042.1 154293 View on NCBI ↗
Campsis radicans NC_073099.1 153630 View on NCBI ↗