Markers + reference

Barclaya

2 species · Nymphaeaceae · Nymphaeales

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Species 2
Genome length 160–160 kb
Candidate markers 261
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 6 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
DR443_pgt001-psbA Genome 488 0.0541 0.91 85.0 yes View details
petN-psbM Genome 1322 0.0076 1.00 63.0 yes View details
psbM-DR443_pgt008 Genome 794 0.0038 0.98 58.4 yes View details
DR443_pgt008-DR443_pgt009 Genome 416 0.0120 1.00 57.6 yes View details
DR443_pgt010-psbD Genome 1552 0.0064 1.00 62.3 yes View details
psbC-DR443_pgt011 Genome 210 0.0286 1.00 68.9 yes View details
DR443_pgt011-psbZ Genome 374 0.0027 1.00 48.6 yes View details
DR443_pgt015-DR443_pgt016 Genome 1483 0.0202 0.97 72.6 yes View details
petD-rpoA Genome 430 0.0233 1.00 68.6 yes View details
rpoA Genome 1011 0.0040 1.00 48.3 yes View details
ycf1 Genome 168 0.0000 0.95 42.5 no View details
ycf1 Genome 5679 0.0044 1.00 55.1 yes View details
ycf1-ndhF Genome 44 0.0263 0.86 69.6 yes View details
DR443_pgt018-atpE Genome 233 0.0182 0.94 66.6 yes View details
matK-DR443_pgt002 Genome 743 0.0054 1.00 61.8 yes View details
atpF Genome 1292 0.0031 1.00 60.9 yes View details
DR443_pgt019-DR443_pgt020 Genome 143 0.0140 1.00 60.5 yes View details
ndhF-rpl32 Genome 1105 0.0018 0.99 60.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
DR443_pgt001-psbA_p1 DR443_pgt001-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 518–554 1.000 84.4
DR443_pgt001-psbA_p2 DR443_pgt001-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 521–557 1.000 84.3
DR443_pgt001-psbA_p3 DR443_pgt001-psbA AATCCACTTGGCTACATCCG TAGACCTAGCTGCTGTCGAA 514–550 1.000 84.0
DR443_pgt001-psbA_p4 DR443_pgt001-psbA AATCCACTTGGCTACATCCG CTAGACCTAGCTGCTGTCGA 515–551 1.000 82.3
DR443_pgt001-psbA_p5 DR443_pgt001-psbA AATCCACTTGGCTACATCCG TCTAGACCTAGCTGCTGTCG 516–552 1.000 82.3
matK-DR443_pgt002_p1 matK-DR443_pgt002 CGCTGTTTCCGGTATCTCTC TTTGACTTGACTGGTTCCGG 910–916 1.000 78.8
matK-DR443_pgt002_p2 matK-DR443_pgt002 TATAGGAAGCGCTGTTTCCG TTTGACTTGACTGGTTCCGG 919–925 1.000 78.3
matK-DR443_pgt002_p3 matK-DR443_pgt002 CGCTGTTTCCGGTATCTCTC TCTGGGTTGCTAACTCAACG 845–851 1.000 77.8
matK-DR443_pgt002_p4 matK-DR443_pgt002 CGCTGTTTCCGGTATCTCTC AACGGTAGAGTACTCGGCTT 829–835 1.000 77.8
matK-DR443_pgt002_p5 matK-DR443_pgt002 CGCTGTTTCCGGTATCTCTC ACGGTAGAGTACTCGGCTTT 828–834 1.000 77.8
DR443_pgt005_p1 DR443_pgt005 CGACAAATGGGCCATTCCTA TCCTCCTTTCCATTCCCTGT 954 1.000 79.3
DR443_pgt005_p2 DR443_pgt005 TCAAGTATCCCCGGAGACAG TCCTCCTTTCCATTCCCTGT 1029 1.000 77.9
DR443_pgt005_p3 DR443_pgt005 GTTCGACAAATGGGCCATTC TCCTCCTTTCCATTCCCTGT 957 1.000 77.5
DR443_pgt005_p4 DR443_pgt005 GCCTCATCTCCTTGTTCGAC TCCTCCTTTCCATTCCCTGT 970 1.000 76.9
DR443_pgt005_p5 DR443_pgt005 TATCTTGATCGCGCCTCATC TCCTCCTTTCCATTCCCTGT 982 1.000 76.9
atpF_p1 atpF TTTCTTCGGCTCGAATGGTT AAGTGTCTTATCGGGGATCT 1485–1490 1.000 57.7
atpF_p2 atpF TCTTCGGCTCGAATGGTTAC AAGTGTCTTATCGGGGATCT 1483–1488 1.000 56.8
atpF_p3 atpF ATTTCTTCGGCTCGAATGGT AAGTGTCTTATCGGGGATCT 1486–1491 1.000 55.9
atpF_p4 atpF TTTCTTCGGCTCGAATGGTT TCGGGGATCTAAATAAGGAGTGA 1475–1480 1.000 53.5
atpF_p5 atpF CTTCGGCTCGAATGGTTACC AAGTGTCTTATCGGGGATCT 1482–1487 1.000 53.4
petN-psbM_p1 petN-psbM GAAAGGGGGCATGATTCACA ATTGCTACTGCGCTGTTCAT 1512 1.000 77.3
petN-psbM_p2 petN-psbM AGAAAGGGGGCATGATTCAC ATTGCTACTGCGCTGTTCAT 1513 1.000 77.3
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 1486 1.000 77.3
petN-psbM_p4 petN-psbM GAAAGGGGGCATGATTCACA TATTGCTACTGCGCTGTTCA 1513 1.000 76.3
petN-psbM_p5 petN-psbM AGAAAGGGGGCATGATTCAC TATTGCTACTGCGCTGTTCA 1514 1.000 76.3
psbM-DR443_pgt008_p1 psbM-DR443_pgt008 ATGAACAGCGCAGTAGCAAT TTCAATTGGTCAGAGCACCG 888–902 1.000 75.6
psbM-DR443_pgt008_p2 psbM-DR443_pgt008 TGAACAGCGCAGTAGCAATA TTCAATTGGTCAGAGCACCG 887–901 1.000 74.7
psbM-DR443_pgt008_p3 psbM-DR443_pgt008 AATGAACAGCGCAGTAGCAA TTCAATTGGTCAGAGCACCG 889–903 1.000 73.9
psbM-DR443_pgt008_p4 psbM-DR443_pgt008 AGAATGAACAGCGCAGTAGC TTCAATTGGTCAGAGCACCG 891–905 1.000 72.6
psbM-DR443_pgt008_p5 psbM-DR443_pgt008 ACTAGAATGAACAGCGCAGT TTCAATTGGTCAGAGCACCG 894–908 1.000 71.7

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
Barclaya kunstleri NC_037718.1 160051 View on NCBI ↗
Barclaya rotundifolia NC_063732.1 159785 View on NCBI ↗