Markers + reference

Beesia

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 158–158 kb
Candidate markers 268
Primer pairs 100

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 300 0.0947 0.95 82.2 yes View details
trnK-UUU-rps16 LSC 781 0.0274 0.93 78.7 yes View details
rps16-trnQ-UUG LSC 1799 0.0205 0.76 60.8 yes View details
trnC-GCA-petN LSC 865 0.0173 1.00 61.1 yes View details
psbZ-trnG-GCC LSC 377 0.0647 0.98 81.2 yes View details
ycf3-trnS-GGA LSC 859 0.0223 0.99 72.3 yes View details
trnT-UGU-trnL-UAA LSC 653 0.0309 0.89 71.7 yes View details
ndhC-trnV-UAC LSC 1168 0.0282 0.94 67.4 yes View details
psbE-petL LSC 1041 0.0156 0.99 56.9 yes View details
ycf1-ndhF SSC 313 0.4444 0.14 61.3 yes View details
ccsA-ndhD SSC 261 0.0425 0.99 70.9 yes View details
rps19-rpl2 IRb 72 0.1228 0.79 87.5 yes View details
trnW-CCA-trnP-UGG LSC 176 0.0455 1.00 78.3 yes View details
rpl14-rpl16 LSC 105 0.0700 0.95 76.3 yes View details
trnS-UGA LSC 93 0.0645 1.00 74.9 yes View details
rps14-psaB LSC 129 0.0388 1.00 74.8 yes View details
rpl2-trnH-GUG IRa 59 0.0682 0.75 72.0 no View details
petD-rpoA LSC 212 0.0330 1.00 71.5 yes View details
rpl16-rps3 LSC 171 0.0247 0.95 71.3 yes View details
ndhK-ndhC LSC 64 0.0312 1.00 70.5 yes View details
ndhF-trnL-UAG SSC 1129 0.0186 0.95 68.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTGCTGTTGAAGTTCCAT 341–356 1.000 86.3
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 354–369 1.000 86.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 355–370 1.000 85.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 356–371 1.000 85.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGGAAGTTATGCATGAGCGT 387–402 1.000 84.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CCTTGAAAAAGGCGCTCAAC 872–909 1.000 82.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAAGGCGCTCAACC 871–908 1.000 82.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 871–908 1.000 82.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 870–907 1.000 82.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGAAAAAGGCGCTCAACCTA 868–905 1.000 82.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ACCGATCATGTCCTTCAAGC GAGGTTCGAATCCTTCCGTC 1468–1888 1.000 84.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1473–1893 1.000 83.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ACCGATCATGTCCTTCAAGC CTCGGAGGTTCGAATCCTTC 1472–1892 1.000 83.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACCGATCATGTCCTT CTCGGAGGTTCGAATCCTTC 1477–1897 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAACCGATCATGTCC GAGGTTCGAATCCTTCCGTC 1475–1895 1.000 82.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 928–929 1.000 80.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 922–923 1.000 79.1
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 946–947 1.000 78.4
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 982–983 1.000 77.8
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 940–941 1.000 76.9
trnS-UGA_p1 trnS-UGA GCCGGGCGAAACAAATAAAG CGGGTGTTTCTACGGATAGTG 219–223 1.000 71.1
trnS-UGA_p2 trnS-UGA GCCGGGCGAAACAAATAAAG CGGGTGTTTCTACGGATAGT 219–223 1.000 70.7
trnS-UGA_p3 trnS-UGA AGCCGGGCGAAACAAATAAA CGGGTGTTTCTACGGATAGTG 220–224 1.000 68.0
trnS-UGA_p4 trnS-UGA AGCCGGGCGAAACAAATAAA CGGGTGTTTCTACGGATAGT 220–224 1.000 67.7
trnS-UGA_p5 trnS-UGA AGCCGGGCGAAACAAATAA CGGGTGTTTCTACGGATAGTG 220–224 1.000 65.6
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTTCTGACGGTTGG CGTCTTCTCCTTGGCAAAGA 534–537 1.000 79.9
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTTCTGACGGTTGGTC CGTCTTCTCCTTGGCAAAGA 532–535 1.000 76.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTTCTGACGGTTGG TACCATTCGACCATATCCGC 507–510 1.000 75.6
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TTGCTTCTTCTGACGGTTGG TTACCATTCGACCATATCCGC 508–511 1.000 73.2
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TGCTTCTTCTGACGGTTGG CGTCTTCTCCTTGGCAAAGA 533–536 1.000 72.7

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
Beesia calthifolia NC_041531.1 158355 View on NCBI ↗
Beesia deltophylla NC_072729.1 157506 View on NCBI ↗