Markers + reference

Piptadenia

2 species · Fabaceae · Fabales

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Species 2
Genome length 163–163 kb
Candidate markers 268
Primer pairs 75

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 6 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 693 0.0000 1.00 25.0 no View details
rpl32-trnL-UAG SSC 458 0.4910 0.85 77.9 yes View details
ndhD SSC 1497 0.4736 0.89 81.8 yes View details
psaC SSC 246 0.5000 0.95 77.2 yes View details
psaC-ndhE SSC 260 0.4798 0.95 77.0 yes View details
ndhG SSC 531 0.4717 0.97 80.6 yes View details
ndhI SSC 486 0.4670 0.81 77.4 yes View details
ndhA SSC 2549 0.4746 0.79 76.9 yes View details
ndhH SSC 1182 0.4925 0.79 79.1 yes View details
ycf1 SSC 5463 0.3838 0.91 76.2 yes View details
ccsA SSC 972 0.4348 0.83 80.4 yes View details
ndhF-rpl32 SSC 954 0.4245 0.81 79.6 yes View details
rps15-ycf1 SSC 407 0.4521 0.90 78.4 yes View details
ndhF SSC 2232 0.4576 0.76 76.8 yes View details
rps15 SSC 273 0.4781 0.92 76.6 yes View details
trnL-UAG-ccsA SSC 89 0.4557 0.89 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhF_p1 ndhF TGTTTCGATGCAACAACCAA TCCCCACTCTCTGGATCTAA 2885 0.500 37.7
ndhF_p2 ndhF TGTTTCGATGCAACAACCAA TCCCCACTCTCTGGATCTAAA 2885 0.500 35.9
ndhF_p3 ndhF ATGTTTCGATGCAACAACCA TCCCCACTCTCTGGATCTAA 2886 0.500 35.9
ndhF_p4 ndhF TGTTTCGATGCAACAACCAA ATCCCCACTCTCTGGATCTA 2886 0.500 35.8
ndhF_p5 ndhF TGTTTCGATGCAACAACCAA TATCCCCACTCTCTGGATCT 2887 0.500 35.8
ndhF-rpl32_p1 ndhF-rpl32 GGGGAATTGGGCAGACTTAG AGCGTGTCTACCGATTTCAC 2344 0.500 59.5
ndhF-rpl32_p2 ndhF-rpl32 GGGGAATTGGGCAGACTTAG CAGCGTGTCTACCGATTTCA 2345 0.500 59.5
ndhF-rpl32_p3 ndhF-rpl32 AAATAACAGGAAGGCGCACA AGCGTGTCTACCGATTTCAC 2311 0.500 59.2
ndhF-rpl32_p4 ndhF-rpl32 AATAACAGGAAGGCGCACAA AGCGTGTCTACCGATTTCAC 2310 0.500 59.2
ndhF-rpl32_p5 ndhF-rpl32 ATAACAGGAAGGCGCACAAA AGCGTGTCTACCGATTTCAC 2309 0.500 59.2
rpl32-trnL-UAG_p1 rpl32-trnL-UAG ACGACCAAGTAACCGGGATA AGCGTGTCTACCGATTTCAC 999 0.500 58.7
rpl32-trnL-UAG_p2 rpl32-trnL-UAG ACGACCAAGTAACCGGGATA CAGCGTGTCTACCGATTTCA 1000 0.500 58.7
rpl32-trnL-UAG_p3 rpl32-trnL-UAG ACGACCAAGTAACCGGGATA GCTGCATAGCCCAATACCAT 1591 0.500 58.1
rpl32-trnL-UAG_p4 rpl32-trnL-UAG ACGACCAAGTAACCGGGATA ATCATGCCTTTTTCGGACGA 1276 0.500 57.9
rpl32-trnL-UAG_p5 rpl32-trnL-UAG ACGACCAAGTAACCGGGATA TGCCTTTTTCGGACGAATCA 1272 0.500 57.9
trnL-UAG-ccsA_p1 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT GCTGCATAGCCCAATACCAT 612 0.500 59.3
trnL-UAG-ccsA_p2 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG GCTGCATAGCCCAATACCAT 611 0.500 59.2
trnL-UAG-ccsA_p3 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT ATCATGCCTTTTTCGGACGA 297 0.500 59.1
trnL-UAG-ccsA_p4 trnL-UAG-ccsA TGAAATCGGTAGACACGCTG ATCATGCCTTTTTCGGACGA 296 0.500 59.1
trnL-UAG-ccsA_p5 trnL-UAG-ccsA GTGAAATCGGTAGACACGCT TGCCTTTTTCGGACGAATCA 293 0.500 59.0
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT GGTGTTTGTGAGAACCCCTT 1585 0.500 59.4
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG GGTGTTTGTGAGAACCCCTT 1584 0.500 59.4
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT TGGGCCCCGAGAGTTATTTA 1866 0.500 59.0
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG TGGGCCCCGAGAGTTATTTA 1865 0.500 59.0
ccsA_p5 ccsA GTGAAATCGGTAGACACGCT CAGTTGACAAGGTCGAAGCT 1780 0.500 58.9
ndhD_p1 ndhD AAACACCAAACGTATCCGGT TGATCGTGTTTGCGAAAACG 2212 0.500 57.8
ndhD_p2 ndhD AAACACCAAACGTATCCGGT GATCGTGTTTGCGAAAACGT 2211 0.500 57.8
ndhD_p3 ndhD AAACACCAAACGTATCCGGT ACGTATGATCGTGTTTGCGA 2217 0.500 57.8
ndhD_p4 ndhD AAACACCAAACGTATCCGGT TCTGCTCCAAGAACAGAGGA 1910 0.500 57.8
ndhD_p5 ndhD AAACACCAAACGTATCCGGT AAACAACTCGAAGCATGGGT 1816 0.500 57.8

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
Piptadenia communis NC_034990.1 162552 View on NCBI ↗
Piptadenia gonoacantha PV870779.1 162552 View on NCBI ↗