Markers + reference

Caulophyllum

2 species · Berberidaceae · Ranunculales

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Species 2
Genome length 157–158 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

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5619 0.3744 0.83 74.1 yes View details
ndhH SSC 1182 0.4771 0.87 81.3 yes View details
ndhA SSC 2165 0.4763 0.81 78.2 yes View details
ndhD SSC 1533 0.4931 0.90 82.0 yes View details
ndhD-ccsA SSC 551 0.4491 0.52 71.7 yes View details
ndhF SSC 2229 0.4718 0.86 79.6 yes View details
ycf1 IRa 1062 0.0009 1.00 44.6 no View details
psbT-psbN LSC 74 0.1081 1.00 87.5 yes View details
rpl32-ndhF SSC 1142 0.4557 0.90 82.2 yes View details
trnL-UAG-rpl32 SSC 1011 0.4573 0.88 81.6 yes View details
ndhI-ndhG SSC 548 0.4237 0.91 81.4 yes View details
ndhI SSC 552 0.4598 0.88 80.6 yes View details
ccsA SSC 972 0.4692 0.78 79.0 yes View details
rpl32 SSC 165 0.4744 0.95 77.3 yes View details
psaC SSC 246 0.4868 0.93 76.8 yes View details
ndhE SSC 306 0.4695 0.91 76.4 yes View details
ccsA-trnL-UAG SSC 99 0.3667 0.91 76.2 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
psbT-psbN_p1 psbT-psbN TTTCGAGAACCACCTAAGGT ACCCTAGTCGCCATCTTTCT 236 1.000 66.4
psbT-psbN_p2 psbT-psbN TTTCGAGAACCACCTAAGGT GATCCATTCGAGGAACACGG 143 1.000 65.8
psbT-psbN_p3 psbT-psbN TTTTCGAGAACCACCTAAGGT ACCCTAGTCGCCATCTTTCT 237 1.000 64.6
psbT-psbN_p4 psbT-psbN TTTCGAGAACCACCTAAGGT GGCAACCCTCTCAACAACTA 166 1.000 64.1
psbT-psbN_p5 psbT-psbN AGGTTCCAACTAAAAGGGTCA ACCCTAGTCGCCATCTTTCT 220 1.000 63.9
ycf1_p1 ycf1 AGTCCTTTCCTCATTTGCGG TTTCGGGGAGAACCAAAAGG 1068 0.500 58.5
ycf1_p2 ycf1 GTCCTTTCCTCATTTGCGGA TTTCGGGGAGAACCAAAAGG 1067 0.500 58.5
ycf1_p3 ycf1 AGTCCTTTCCTCATTTGCGG GTGCCAAGGTTTCAGACAGA 949 0.500 58.3
ycf1_p4 ycf1 AGTCCTTTCCTCATTTGCGG TCTGTGCCAAGGTTTCAGAC 952 0.500 58.3
ycf1_p5 ycf1 GTCCTTTCCTCATTTGCGGA GTGCCAAGGTTTCAGACAGA 948 0.500 58.3
ndhH_p1 ndhH TCAGAGGGGTTTGCGAAAAA CCCGAGACTGAATAAACGCA 1749 0.500 59.5
ndhH_p2 ndhH TCAGAGGGGTTTGCGAAAAA AGTGTCCTAACGAATCGCAC 2019 0.500 59.5
ndhH_p3 ndhH TCAGAGGGGTTTGCGAAAAA TTAGTTCATCGCCCCGAATG 2121 0.500 59.1
ndhH_p4 ndhH TCAGAGGGGTTTGCGAAAAA TGAAGAATTCCCAAAGGGCC 1667 0.500 59.0
ndhH_p5 ndhH TATCTCAGAGGGGTTTGCGA CCCGAGACTGAATAAACGCA 1753 0.500 58.8
ndhA_p1 ndhA TGTGAGAGTAGAAGCCCCAA TGACCAATATACCTTGCGGC 2517 0.500 59.5
ndhA_p2 ndhA TGTGAGAGTAGAAGCCCCAA CTCGGACTGTTTGTTGACCA 2498 0.500 59.4
ndhA_p3 ndhA TGTGAGAGTAGAAGCCCCAA GGCATACACGAACACAGACT 2669 0.500 59.2
ndhA_p4 ndhA AAATTGGGGCTTATCCGGAC TGACCAATATACCTTGCGGC 2853 0.500 59.2
ndhA_p5 ndhA AAATTGGGGCTTATCCGGAC CTCGGACTGTTTGTTGACCA 2834 0.500 59.0
ndhI_p1 ndhI TTTTGGGGGTGGAATCTGTG GCTGCGATTCTCACAACCTA 1206 0.500 59.9
ndhI_p2 ndhI GGTTTTTGGGGGTGGAATCT GCTGCGATTCTCACAACCTA 1209 0.500 59.7
ndhI_p3 ndhI GGAATCTCGCTATTCCGGAC GCTGCGATTCTCACAACCTA 977 0.500 59.4
ndhI_p4 ndhI ACAGTTCTTTACTTGGGCGG GCTGCGATTCTCACAACCTA 999 0.500 59.1
ndhI_p5 ndhI CAGTTCTTTACTTGGGCGGT GCTGCGATTCTCACAACCTA 998 0.500 59.1
ndhI-ndhG_p1 ndhI-ndhG TGGTCAACAAACAGTCCGAG AATCCCAAGTTGTTGACCCC 1506 0.500 59.5
ndhI-ndhG_p2 ndhI-ndhG AGTCTGTGTTCGTGTATGCC AATCCCAAGTTGTTGACCCC 1335 0.500 59.3
ndhI-ndhG_p3 ndhI-ndhG TGCCCTATTGATCTACCCGT AATCCCAAGTTGTTGACCCC 1319 0.500 59.1
ndhI-ndhG_p4 ndhI-ndhG TGGTCAACAAACAGTCCGAG AATCCCGTACCAGGACGTAT 1437 0.500 59.0
ndhI-ndhG_p5 ndhI-ndhG TGGTCAACAAACAGTCCGAG ATAATCCCGTACCAGGACGT 1439 0.500 59.0

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
Caulophyllum robustum NC_042221.1 157347 View on NCBI ↗
Caulophyllum thalictroides NC_065736.1 157933 View on NCBI ↗