Markers + reference

Dalea

2 species · Fabaceae · Fabales

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Species 2
Genome length 156–156 kb
Candidate markers 257
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 9 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5328 0.4066 0.85 74.5 yes View details
ndhH SSC 1182 0.4950 0.93 83.1 yes View details
ndhA SSC 2301 0.4491 0.81 78.0 yes View details
psaC SSC 246 0.5112 0.72 71.0 yes View details
psaC-ccsA SSC 1882 0.4724 0.82 79.2 yes View details
ccsA SSC 972 0.4841 0.87 81.4 yes View details
ndhF SSC 2226 0.4681 0.82 78.4 yes View details
trnL-UAG-rpl32 SSC 673 0.4271 0.86 80.9 yes View details
atpF-atpH LSC 644 0.0333 0.98 79.9 yes View details
rpl32-ndhF SSC 630 0.3721 0.82 79.9 yes View details
ndhI-ndhG SSC 476 0.4302 0.90 79.8 yes View details
psbZ-trnG-GCC LSC 565 0.0412 0.99 79.5 yes View details
ndhG SSC 531 0.4163 0.83 78.8 yes View details
ndhI SSC 483 0.4819 0.86 78.6 yes View details
ycf1-rps15 SSC 414 0.4259 0.90 78.2 yes View details
rps15-ndhH SSC 107 0.4554 0.94 77.2 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
atpF-atpH_p1 atpF-atpH CCAGTAACCCAAGCAAAGGA GGCTGGTTGTAGCATTAGCA 723–733 1.000 79.6
atpF-atpH_p2 atpF-atpH CCAGTAACCCAAGCAAAGGA TGGGCTGGTTGTAGCATTAG 725–735 1.000 78.2
atpF-atpH_p3 atpF-atpH CCAGTAACCCAAGCAAAGGA AGGCAGAGGGAAAAATACGG 792–802 1.000 77.9
atpF-atpH_p4 atpF-atpH CCAGTAACCCAAGCAAAGGA CCTGAGGCAGAGGGAAAAAT 796–806 1.000 77.0
atpF-atpH_p5 atpF-atpH CCAGTAACCCAAGCAAAGGA GCAGAGGGAAAAATACGGGG 790–800 1.000 76.3
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG CGTCTTCTCCTTGGCAAAGA 716–719 1.000 81.9
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 719–722 1.000 80.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TCCTGATGGTTGGTCGAGTA CGTCTTCTCCTTGGCAAAGA 712–715 1.000 80.2
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 717–720 1.000 79.9
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTCTCCTGATGGTTGGTCGA CGTCTTCTCCTTGGCAAAGA 715–718 1.000 79.1
ycf1_p1 ycf1 AACAGAATACGCGGATCGAG AGCCAAAGCCTTACAGCAAT 748 0.500 58.5
ycf1_p2 ycf1 TAACCCGTGGATCATACCCA AGCCAAAGCCTTACAGCAAT 916 0.500 58.0
ycf1_p3 ycf1 AACAGAATACGCGGATCGAG CCTACGACGTCTAGCGGATA 640 0.500 57.3
ycf1_p4 ycf1 ACAGGCCTTTCGTTGATTCA AGCCAAAGCCTTACAGCAAT 300 0.500 57.3
ycf1_p5 ycf1 TCACAGGCCTTTCGTTGATT AGCCAAAGCCTTACAGCAAT 302 0.500 57.3
ycf1-rps15_p1 ycf1-rps15 ATTGCTGTAAGGCTTTGGCT AACACCATGCATTGATGGGT 1060 0.500 59.0
ycf1-rps15_p2 ycf1-rps15 ATTGCTGTAAGGCTTTGGCT TGCCATAAAAGGTCCCAACC 1354 0.500 58.9
ycf1-rps15_p3 ycf1-rps15 ATTGCTGTAAGGCTTTGGCT ATTTCCCAACAGTTCCGGTC 1258 0.500 58.7
ycf1-rps15_p4 ycf1-rps15 ATTGCTGTAAGGCTTTGGCT CCGATCCGTGGTTTTCTTCT 678 0.500 58.7
ycf1-rps15_p5 ycf1-rps15 ATTGCTGTAAGGCTTTGGCT TAATCGTTGCCGTTTTCCCA 803 0.500 58.6
rps15-ndhH_p1 rps15-ndhH AAAACCACGGATCGGTTGAA AACACCATGCATTGATGGGT 397 0.500 59.3
rps15-ndhH_p2 rps15-ndhH AAAACCACGGATCGGTTGAA TGCCATAAAAGGTCCCAACC 691 0.500 59.2
rps15-ndhH_p3 rps15-ndhH AAAACCACGGATCGGTTGAA ATTTCCCAACAGTTCCGGTC 595 0.500 59.0
rps15-ndhH_p4 rps15-ndhH AAAACCACGGATCGGTTGAA ATCGGTCCTGATAAACCCCA 990 0.500 58.9
rps15-ndhH_p5 rps15-ndhH AGAAGAAAACCACGGATCGG AACACCATGCATTGATGGGT 402 0.500 58.8
ndhH_p1 ndhH AAAACCACGGATCGGTTGAA CTAGGAAAGCGGCATAGCAA 2113 0.500 59.4
ndhH_p2 ndhH AAAACCACGGATCGGTTGAA CGTTGTTGTATCCCTGCAGA 1687 0.500 59.0
ndhH_p3 ndhH AAAACCACGGATCGGTTGAA AAGCGGCATAGCAATAGCAT 2107 0.500 59.0
ndhH_p4 ndhH AAAACCACGGATCGGTTGAA GCTTGAAGAACTCCTCCAGG 1729 0.500 58.9
ndhH_p5 ndhH AGAAGAAAACCACGGATCGG CTAGGAAAGCGGCATAGCAA 2118 0.500 58.9

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
Dalea aurea PP887592.1 155924 View on NCBI ↗
Dalea candida PV870769.1 155566 View on NCBI ↗