Markers + reference

Zamia

2 species · Zamiaceae · Cycadales

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Species 2
Genome length 165–165 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
chlL Genome 873 0.5093 0.92 82.8 yes View details
chlN Genome 837 0.4878 0.83 80.3 yes View details
chlN-ycf1 Genome 2283 0.4929 0.87 79.6 yes View details
ycf1 Genome 3630 0.4781 0.89 77.7 yes View details
ndhH Genome 1182 0.4633 0.80 79.3 yes View details
ndhG Genome 543 0.4948 0.71 75.8 yes View details
ndhE Genome 303 0.4905 0.69 70.3 yes View details
ndhD Genome 1503 0.4753 0.85 80.7 yes View details
ccsA Genome 966 0.4892 0.81 79.9 yes View details
trnP-GGG-rpl32 Genome 1288 0.4939 0.83 80.1 yes View details
ndhF Genome 2208 0.4689 0.66 74.1 yes View details
psbF-psbE Genome 9 0.1111 1.00 87.5 yes View details
ndhI Genome 558 0.4637 0.91 81.9 yes View details
trnN-GTT-chlL Genome 1225 0.1599 0.99 80.5 yes View details
rpl32-ndhF Genome 1173 0.4631 0.82 79.9 yes View details
ndhA Genome 2107 0.4768 0.84 79.4 yes View details
ycf1-rps15 Genome 430 0.4563 0.96 79.3 yes View details
psaC-ndhD Genome 138 0.4077 0.94 77.1 yes View details
ndhE-psaC Genome 469 0.4868 0.81 76.9 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbF-psbE_p1 psbF-psbE GAACGGCCAACCATCTAACT AGAGTCGACAAGAGGTTCCA 141 1.000 79.7
psbF-psbE_p2 psbF-psbE GTACAGCTAGTCCGTGAACG AGAGTCGACAAGAGGTTCCA 156 1.000 79.6
psbF-psbE_p3 psbF-psbE AACGGCCAACCATCTAACTG AGAGTCGACAAGAGGTTCCA 140 1.000 79.1
psbF-psbE_p4 psbF-psbE GTGAACGGCCAACCATCTAA AGAGTCGACAAGAGGTTCCA 143 1.000 79.1
psbF-psbE_p5 psbF-psbE TGAACGGCCAACCATCTAAC AGAGTCGACAAGAGGTTCCA 142 1.000 79.1
trnN-GTT-chlL_p1 trnN-GTT-chlL TGAACCTACGACCAGTCAGT TCAATGGAGCAGCAAAACCT 1690 0.500 59.9
trnN-GTT-chlL_p2 trnN-GTT-chlL TTTCGTACAGTACCCCTGGT TCAATGGAGCAGCAAAACCT 2309 0.500 59.9
trnN-GTT-chlL_p3 trnN-GTT-chlL TGAACCTACGACCAGTCAGT GACCAAGCCTGCTAATCGAA 1815 0.500 59.7
trnN-GTT-chlL_p4 trnN-GTT-chlL TGAACCTACGACCAGTCAGT GATGGCTCGGATTCAACCAT 1964 0.500 59.7
trnN-GTT-chlL_p5 trnN-GTT-chlL TTTCGTACAGTACCCCTGGT GACCAAGCCTGCTAATCGAA 2434 0.500 59.7
chlL_p1 chlL CGGTCCTTTCATCTCTCTGC CCAACCTGATACCTTGACGG 2290 0.500 59.3
chlL_p2 chlL GGATCATGGGCTGGTTGAAT CCAACCTGATACCTTGACGG 2243 0.500 59.2
chlL_p3 chlL CGGTCCTTTCATCTCTCTGC CGAGGCTCTGCAAAGATCAT 1809 0.500 59.1
chlL_p4 chlL CGGTCCTTTCATCTCTCTGC TTCAGAGATCTCCACTGGCA 1639 0.500 59.0
chlL_p5 chlL GGATCATGGGCTGGTTGAAT CGAGGCTCTGCAAAGATCAT 1762 0.500 59.0
chlN_p1 chlN AGGTTTTGCTGCTCCATTGA CGGGTTGTAACTCACGCATA 1705 0.500 60.0
chlN_p2 chlN TTCGATTAGCAGGCTTGGTC CGGGTTGTAACTCACGCATA 1580 0.500 59.8
chlN_p3 chlN ATGGTTGAATCCGAGCCATC CGGGTTGTAACTCACGCATA 1431 0.500 59.8
chlN_p4 chlN ACTTCGATTAGCAGGCTTGG CGGGTTGTAACTCACGCATA 1582 0.500 59.8
chlN_p5 chlN CTTCGATTAGCAGGCTTGGT CGGGTTGTAACTCACGCATA 1581 0.500 59.8
chlN-ycf1_p1 chlN-ycf1 CCGTCAAGGTATCAGGTTGG CGCAAAGGGCAGGAATATCT 2886 0.500 59.6
chlN-ycf1_p2 chlN-ycf1 CCGTCAAGGTATCAGGTTGG CCATCTCATGGGACTTGTGG 2741 0.500 59.4
chlN-ycf1_p3 chlN-ycf1 GGTTGGTTACCCGCTCATAG CGCAAAGGGCAGGAATATCT 2872 0.500 59.4
chlN-ycf1_p4 chlN-ycf1 GGTTGGTTACCCGCTCATAG CCATCTCATGGGACTTGTGG 2727 0.500 59.2
chlN-ycf1_p5 chlN-ycf1 TACTCAGGGGGAAGACACTG CCATCTCATGGGACTTGTGG 2965 0.500 59.1
ycf1_p1 ycf1 AGACTCTTTGGAAATGGCTTCA CGCAAAGGGCAGGAATATCT 359 0.500 42.9
ycf1_p2 ycf1 AGACTCTTTGGAAATGGCTTCA GCCATCTGTCCGGAAATTCT 1058 0.500 42.8
ycf1_p3 ycf1 AGACTCTTTGGAAATGGCTTCA CCGTTCGGGTCGATAATTGT 519 0.500 42.6
ycf1_p4 ycf1 AGACTCTTTGGAAATGGCTTCA CCTGATCTTTCTTGGGCGAA 493 0.500 42.3
ycf1_p5 ycf1 AGACTCTTTGGAAATGGCTTCA TCTCTGTATTCCGTTCGGGT 529 0.500 41.9

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
Zamia fischeri MH311043.1 164767 View on NCBI ↗
Zamia furfuracea NC_026040.1 164953 View on NCBI ↗