Markers + reference

Vancouveria

2 species · Berberidaceae · Ranunculales

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Species 2
Genome length 157–158 kb
Candidate markers 269
Primer pairs 75

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD-psaI LSC 897 0.0161 0.97 71.2 yes View details
trnP-UGG-psaJ LSC 356 0.0201 0.98 61.9 yes View details
psaJ-rpl33 LSC 421 0.0190 1.00 51.2 yes View details
clpP LSC 2164 0.0065 1.00 47.8 yes View details
rpl16 LSC 1569 0.1334 0.99 80.0 yes View details
rps3 LSC 666 0.1784 0.98 80.3 yes View details
ndhD SSC 1503 0.0007 1.00 47.5 yes View details
psbT-psbN LSC 66 0.1061 1.00 87.5 yes View details
ndhD-psaC SSC 135 0.0746 0.99 85.0 yes View details
rpl16-rps3 LSC 199 0.4932 0.74 71.5 yes View details
rpl23 IRa 33 0.0303 1.00 69.9 no View details
rpl32 SSC 123 0.0163 1.00 61.8 yes View details
ccsA-ndhD SSC 202 0.0297 1.00 60.7 yes View details
trnT-GGU-psbD LSC 1177 0.0017 0.99 60.6 yes View details
trnT-UGU-trnL-UAA LSC 862 0.0023 1.00 60.1 yes View details
rpl23 LSC 309 0.0065 1.00 56.4 no 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
trnT-GGU-psbD_p1 trnT-GGU-psbD AAGCGAATGGGCCCTTTTAA ACAAAAACGAAACGGTCCCT 1341–1351 1.000 78.2
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1331–1341 1.000 77.9
trnT-GGU-psbD_p3 trnT-GGU-psbD ATGGGCCCTTTTAACTCAGC ACAAAAACGAAACGGTCCCT 1335–1345 1.000 77.6
trnT-GGU-psbD_p4 trnT-GGU-psbD AAGCGAATGGGCCCTTTTAA CAAAAACGAAACGGTCCCTC 1340–1350 1.000 77.0
trnT-GGU-psbD_p5 trnT-GGU-psbD AAGCGAATGGGCCCTTTTAA ATAAGCCGGACCAACCTACA 1358–1368 1.000 76.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA CTCTAACCGCTGAGCTAAGC ACCAATTTCGCCATATCCCC 906 1.000 78.9
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA CTCTAACCGCTGAGCTAAGC TAGCGTCTACCAATTTCGCC 914 1.000 78.4
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 944 1.000 78.2
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 952 1.000 77.7
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA CAAATGCGATGCTCTAACCG ACCAATTTCGCCATATCCCC 917 1.000 77.1
trnV-UAC_p1 trnV-UAC TGAGAAAAGTGAAAAGTATACTACA TGAGAGATCAATCATGTCTTGTCA 862–869 1.000 42.8
trnV-UAC_p2 trnV-UAC TGAGAAAAGTGAAAAGTATACTACA AGCAATATTCTCACAGGAAACA 886–893 1.000 42.7
trnV-UAC_p3 trnV-UAC TGAGAAAAGTGAAAAGTATACTACA TCTCACAGGAAACATATGAGAGA 878–885 1.000 42.7
trnV-UAC_p4 trnV-UAC TGAGAAAAGTGAAAAGTATACTACA AAGCAATATTCTCACAGGAAACA 887–894 1.000 42.7
trnV-UAC_p5 trnV-UAC TGAGAAAAGTGAAAAGTATACTACAA AGCAATATTCTCACAGGAAACA 886–893 1.000 42.7
accD-psaI_p1 accD-psaI AAGGCGTTCTGAGTGAGTTG ACTAGGCCCACGATAGGTAC 1003–1033 1.000 82.4
accD-psaI_p2 accD-psaI AAGGCGTTCTGAGTGAGTTG CTAGGCCCACGATAGGTACA 1002–1032 1.000 82.4
accD-psaI_p3 accD-psaI AAGGCGTTCTGAGTGAGTTG GCAGGAAATACTAGGCCCAC 1012–1042 1.000 82.1
accD-psaI_p4 accD-psaI AAGGCGTTCTGAGTGAGTTG AGGAAATACTAGGCCCACGA 1010–1040 1.000 81.0
accD-psaI_p5 accD-psaI AAGGCGTTCTGAGTGAGTTG CAGGAAATACTAGGCCCACG 1011–1041 1.000 80.5
trnP-UGG-psaJ_p1 trnP-UGG-psaJ ACCCGTGACATTTTGTACCC AAACCTGCCAAAGACCCAAA 485 1.000 80.5
trnP-UGG-psaJ_p2 trnP-UGG-psaJ CCCGTGACATTTTGTACCCA AAACCTGCCAAAGACCCAAA 484 1.000 80.5
trnP-UGG-psaJ_p3 trnP-UGG-psaJ ACAGGATTTGAACCCGTGAC AAACCTGCCAAAGACCCAAA 496 1.000 80.4
trnP-UGG-psaJ_p4 trnP-UGG-psaJ CAGGATTTGAACCCGTGACA AAACCTGCCAAAGACCCAAA 495 1.000 80.4
trnP-UGG-psaJ_p5 trnP-UGG-psaJ TGACAGGATTTGAACCCGTG AAACCTGCCAAAGACCCAAA 498 1.000 80.4
psaJ-rpl33_p1 psaJ-rpl33 ACCCGTGACATTTTGTACCC TACATACGCGCGCTCTTTAA 1195–1221 1.000 79.2
psaJ-rpl33_p2 psaJ-rpl33 CCCGTGACATTTTGTACCCA TACATACGCGCGCTCTTTAA 1194–1220 1.000 79.2
psaJ-rpl33_p3 psaJ-rpl33 ACAGGATTTGAACCCGTGAC TACATACGCGCGCTCTTTAA 1206–1232 1.000 79.1
psaJ-rpl33_p4 psaJ-rpl33 CAGGATTTGAACCCGTGACA TACATACGCGCGCTCTTTAA 1205–1231 1.000 79.1
psaJ-rpl33_p5 psaJ-rpl33 ATGCGTTGACATTCCCCTTT TACATACGCGCGCTCTTTAA 681–707 1.000 78.9

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
Vancouveria hexandra NC_042222.1 156882 View on NCBI ↗
Vancouveria planipetala MH337373.1 157698 View on NCBI ↗