Markers + reference

Prioria

2 species · Fabaceae · Fabales

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Species 2
Genome length 160–161 kb
Candidate markers 267
Primer pairs 100

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 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 842 0.0581 0.94 85.3 yes View details
atpF-atpH LSC 898 0.0584 0.72 73.2 yes View details
psbZ-trnG-UCC LSC 817 0.1132 0.91 87.9 yes View details
trnG-UCC-trnfM-CAU LSC 249 0.1745 0.94 83.2 yes View details
rps4-trnT-UGU LSC 723 0.0982 0.85 88.7 yes View details
trnT-UGU-trnL-UAA LSC 655 0.0600 0.97 88.9 yes View details
trnM-CAU-atpE LSC 301 0.1051 0.92 85.8 yes View details
rps3-rps19 LSC 751 0.0485 0.99 80.9 yes View details
trnR-ACG-trnN-GUU IRb 855 0.0437 0.83 71.7 yes View details
rpl32-trnL-UAG SSC 1364 0.0436 0.96 76.2 yes View details
ndhG-ndhI SSC 568 0.0661 0.85 76.0 yes View details
trnN-GUU-trnR-ACG IRa 855 0.0437 0.83 71.7 yes View details
trnR-UCU-atpA LSC 402 0.0585 0.94 81.0 yes View details
petA-psbJ LSC 764 0.0414 0.98 79.1 yes View details
ndhD-psaC SSC 127 0.1120 0.98 78.9 yes View details
accD-psaI LSC 579 0.0455 0.95 76.8 yes View details
psbI-trnS-GCU LSC 287 0.0563 0.99 75.7 yes View details
psbF-psbE LSC 9 0.1111 1.00 75.6 yes View details
trnF-GAA-ndhJ LSC 747 0.0245 0.98 74.5 yes View details
psbC-trnS-UGA LSC 234 0.0641 1.00 73.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbI-trnS-GCU_p1 psbI-trnS-GCU TCCTATCTAACGATCCGGGAC ATTTTCGTACCGAGGGTTCG 367–554 1.000 73.6
psbI-trnS-GCU_p2 psbI-trnS-GCU TCCTATCTAACGATCCGGGAC TGGACTAAAGCGTCGGATTG 404–591 1.000 73.3
psbI-trnS-GCU_p3 psbI-trnS-GCU TCCTATCTAACGATCCGGGAC GTGGACTAAAGCGTCGGATT 405–592 1.000 73.3
psbI-trnS-GCU_p4 psbI-trnS-GCU TCCTATCTAACGATCCGGGA ATTTTCGTACCGAGGGTTCG 367–554 1.000 73.2
psbI-trnS-GCU_p5 psbI-trnS-GCU TCCTATCTAACGATCCGGGA TGGACTAAAGCGTCGGATTG 404–591 1.000 72.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TGAATCAAACGAGGTACCCC 954–955 1.000 81.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TGAATCAAACGAGGTACCCC 953–954 1.000 81.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAGATTAGCAATCCGACGCT TGAATCAAACGAGGTACCCC 962–963 1.000 80.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA TGAATCAAACGAGGTACCCC 1008–1009 1.000 80.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAATCAAACGAGGTACCCCT 953–954 1.000 79.2
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTTACCGGGGAAGCAGAA 511–516 1.000 72.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTTACCGGGGAAGC 515–520 1.000 72.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 501–506 1.000 70.9
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATTTACCGGGGAAGCAGAAG 510–515 1.000 70.5
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CATTTACCGGGGAAGCAGAA 546–551 1.000 69.6
atpF-atpH_p1 atpF-atpH CCCAAAGAAAGGAAAGAATCGG AGGCAGAGGGAAAAATACGG 842–1049 1.000 64.3
atpF-atpH_p2 atpF-atpH CCCAAAGAAAGGAAAGAATCGG CCTGAGGCAGAGGGAAAAAT 846–1053 1.000 63.5
atpF-atpH_p3 atpF-atpH CCCAAAGAAAGGAAAGAATCGG GCAGAGGGAAAAATACGGGG 840–1047 1.000 62.8
atpF-atpH_p4 atpF-atpH CCCAAAGAAAGGAAAGAATCGG GGCAGAGGGAAAAATACGGG 841–1048 1.000 62.8
atpF-atpH_p5 atpF-atpH CCCAAAGAAAGGAAAGAATCGG CAGAGGGAAAAATACGGGGT 839–1046 1.000 61.3
psbC-trnS-UGA_p1 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGGTTCGAATCCCTCTCTCT 330 1.000 78.9
psbC-trnS-UGA_p2 psbC-trnS-UGA GCTGCAGCAGGATTTGAAAA GGGTTCGAATCCCTCTCTCT 329 1.000 78.4
psbC-trnS-UGA_p3 psbC-trnS-UGA TAGGTCATTTATGGCACGCG GGGTTCGAATCCCTCTCTCT 364 1.000 78.2
psbC-trnS-UGA_p4 psbC-trnS-UGA GTAGGTCATTTATGGCACGC GGGTTCGAATCCCTCTCTCT 365 1.000 73.2
psbC-trnS-UGA_p5 psbC-trnS-UGA CAGCTGCAGCAGGATTTGAA GGGTTCGAATCCCTCTCTCT 331 1.000 73.0
psbZ-trnG-UCC_p1 psbZ-trnG-UCC GATGGTTGGTCGAGTAACAA CGTCTTCTCCTTGGCAAAGA 963–987 1.000 68.8
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GATGGTTGGTCGAGTAACAAA CGTCTTCTCCTTGGCAAAGA 963–987 1.000 67.1
psbZ-trnG-UCC_p3 psbZ-trnG-UCC GATGGTTGGTCGAGTAACAA GGATAGCGGGAATTGAACCC 984–1008 1.000 66.9
psbZ-trnG-UCC_p4 psbZ-trnG-UCC TGGTTGGTCGAGTAACAAAA CGTCTTCTCCTTGGCAAAGA 961–985 1.000 66.7
psbZ-trnG-UCC_p5 psbZ-trnG-UCC GATGGTTGGTCGAGTAACAA AATTGAACCCGCGTCTTCTC 974–998 1.000 65.6

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
Prioria balsamifera MZ274106.1 160989 View on NCBI ↗
Prioria oxyphylla MZ274107.1 160136 View on NCBI ↗