Markers + reference

Bursera

5 species · Burseraceae · Sapindales

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Species 5
Genome length 160–160 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1046 0.0113 1.00 53.6 yes View details
rps16-trnQ-UUG LSC 1595 0.0179 1.00 64.1 yes View details
psbZ-trnG-GCC LSC 448 0.0125 1.00 56.0 yes View details
trnT-UGU-trnL-UAA LSC 980 0.0145 1.00 71.7 yes View details
trnF-GAA-ndhJ LSC 677 0.0193 1.00 62.5 yes View details
ndhF-rpl32 SSC 1065 0.0151 1.00 47.3 yes View details
ccsA-ndhD SSC 326 0.0374 0.98 68.9 yes View details
ycf1-trnN-GUU SSC 3822 0.0083 1.00 50.6 yes View details
trnS-GCU-trnG-UCC LSC 948 0.0120 1.00 66.4 yes View details
trnG-GCC-trnfM-CAU LSC 180 0.0267 1.00 65.1 yes View details
petA-psbJ LSC 1130 0.0097 1.00 60.9 yes View details
psaI-pafII LSC 454 0.0110 1.00 59.3 yes View details
psbB-psbT LSC 198 0.0091 1.00 58.2 yes View details
trnD-GUC-trnY-GUA LSC 491 0.0067 1.00 58.0 yes View details
trnR-UCU-atpA LSC 165 0.0315 1.00 57.7 yes View details
petN-psbM LSC 639 0.0098 0.95 56.3 yes View details
psbE-petL LSC 1443 0.0072 1.00 56.0 yes View details
psbM-trnD-GUC LSC 533 0.0122 1.00 55.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1459–1486 1.000 81.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CAAAAAGGGGTGTGTTGCTG 1866–1901 1.000 81.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CAAAAAGGGGTGTGTTGCTG 1862–1897 1.000 81.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT CAAAAAGGGGTGTGTTGCTG 1863–1898 1.000 81.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CAAAAAGGGGTGTGTTGCTG 1832–1867 1.000 81.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1726–1766 1.000 81.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1668–1708 1.000 81.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATTGAAATGGGGCGTGG 1737–1777 1.000 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1679–1719 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAAATTGAAATGGGGCGTGG 1747–1787 1.000 79.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA AACGGAAGGACCCCTTAACT 1045–1065 1.000 81.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GATACCAAGCCAGCAATGGA AACGGAAGGACCCCTTAACT 1124–1144 1.000 81.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGATACCAAGCCAGCAATGG AACGGAAGGACCCCTTAACT 1125–1145 1.000 81.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACGGAAGGACCCCTTAACT 1103–1123 1.000 80.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC AACGGAAGGACCCCTTAACT 1042–1062 1.000 79.8
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CGAGGAAGCAGAAACCCTTT 520–527 1.000 82.5
trnR-UCU-atpA_p2 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CATTCACCGAGGAAGCAGAA 527–534 1.000 82.4
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG AAGACATTCACCGAGGAAGC 531–538 1.000 82.4
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG ATGAAACAAGTAGCCGGCAA 843–850 1.000 81.4
trnR-UCU-atpA_p5 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TGGAAAGAGCCGCGAAATTA 1073–1080 1.000 80.9
petN-psbM_p1 petN-psbM GCAAAGGTCTTGGGTCAGAA AGTGGAAAGCGCTTAGATGG 1287–1317 1.000 83.7
petN-psbM_p2 petN-psbM TTCAGCAAAGGTCTTGGGTC AGTGGAAAGCGCTTAGATGG 1291–1321 1.000 83.7
petN-psbM_p3 petN-psbM TGAAAGTCTCTGAGTGCACG AGTGGAAAGCGCTTAGATGG 1532–1563 1.000 82.3
petN-psbM_p4 petN-psbM GCAAAGGTCTTGGGTCAGAA GGAAGTGGAAAGCGCTTAGA 1290–1320 0.800 74.4
petN-psbM_p5 petN-psbM TTCAGCAAAGGTCTTGGGTC GGAAGTGGAAAGCGCTTAGA 1294–1324 0.800 74.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TCCCCGGGATTGTAGTTCAA 658–665 1.000 61.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCCCCGGGATTGTAGTTCA 659–666 1.000 61.1
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 643–650 1.000 60.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTTGATTTCCCCGGGATTGT 665–672 1.000 58.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TCCCCGGGATTGTAGTTCAA 665–672 1.000 58.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Bursera bipinnata NC_085818.1 159865 View on NCBI ↗
Bursera cuneata NC_085819.1 159824 View on NCBI ↗
Bursera fagaroides OQ730224.1 159786 View on NCBI ↗
Bursera palmeri NC_085820.1 159872 View on NCBI ↗
Bursera paradoxa PX220297.1 159851 View on NCBI ↗