Markers + reference

Boswellia

7 species · Burseraceae · Sapindales

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Species 7
Genome length 159–161 kb
Candidate markers 273
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1056 0.0245 1.00 66.2 yes View details
trnF-GAA-ndhJ LSC 574 0.0160 1.00 71.4 yes View details
clpP LSC 2062 0.0056 1.00 47.9 yes View details
ycf1 IRb 822 0.0042 1.00 39.7 no View details
ndhF SSC 2235 0.0048 1.00 40.8 yes View details
rpl32-trnL-UAG SSC 1234 0.0167 1.00 63.9 yes View details
ccsA-ndhD SSC 333 0.0389 1.00 76.8 yes View details
ndhD SSC 1362 0.0019 1.00 34.8 yes View details
ycf1 SSC 5127 0.0093 1.00 46.5 yes View details
atpF-atpH LSC 516 0.0111 1.00 64.5 yes View details
rpl22-trnH-GUG LSC 68 0.0686 1.00 64.2 no View details
trnC-GCA-petN LSC 743 0.0051 0.99 62.4 yes View details
trnW-CCA-trnP-UGG LSC 193 0.0169 0.99 59.2 yes View details
rpoB-trnC-GCA LSC 1234 0.0039 1.00 57.6 yes View details
clpP-psbB LSC 438 0.0059 1.00 57.6 yes View details
trnS-GCU-trnG-UCC LSC 946 0.0082 0.99 57.5 yes View details
trnR-ACG-trnN-GUU IRb 608 0.0042 1.00 57.3 yes View details
trnN-GUU-trnR-ACG IRa 608 0.0042 1.00 57.3 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTCTTACAAACGCTCCCGAT AAAAAGGCGCTCAACCTACA 1239–1264 1.000 89.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1258–1283 1.000 89.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CTCGTTGCTTTTCGTTTCCC AAAAAGGCGCTCAACCTACA 1444–1490 1.000 88.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTTACAAACGCTCCCGATG AAAAAGGCGCTCAACCTACA 1238–1263 0.857 83.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTTACAAACGCTCCCGATG CAAAAAGGGGTGTGTTGCTG 1850–1874 0.857 80.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA AACTGAAGGACCCCTTAACT 891–1077 1.000 67.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACTGAAGGACCCCTTAACT 949–1135 1.000 65.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA AAACTGAAGGACCCCTTAACT 892–1078 1.000 65.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC AACTGAAGGACCCCTTAACT 888–1074 1.000 65.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGCTTTAATCCACTCAGCCA AACTGAAGGACCCCTTAACT 887–1073 1.000 64.9
atpF-atpH_p1 atpF-atpH CCAGTGAACCAAGGAAACGA CCTGAGGCAGAGGGAAAAAT 643–693 1.000 81.9
atpF-atpH_p2 atpF-atpH CAAATGGCCAGTGAACCAAG CCTGAGGCAGAGGGAAAAAT 650–700 1.000 78.6
atpF-atpH_p3 atpF-atpH CCAGTGAACCAAGGAAACGA TGGACTGGTTGTAGCATTAGC 572–622 1.000 78.2
atpF-atpH_p4 atpF-atpH CCAGTGAACCAAGGAAACGA GCAGAGGGAAAAATACGAGGT 637–687 1.000 78.0
atpF-atpH_p5 atpF-atpH CCAGTGAACCAAGGAAACGA TGAGGCAGAGGGAAAAATACG 641–691 1.000 78.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GCATTTCCATCTCCGAGCAT TTGTTAATCAGGCGACACCC 1329–1342 1.000 77.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GCATTTCCATCTCCGAGCAT AAAAGGATTTGCAGTCCCCC 1293–1306 1.000 75.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTTCCGCATTTCCATCTCCG TTGTTAATCAGGCGACACCC 1334–1347 1.000 75.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GCATTTCCATCTCCGAGCAT GCGACACCCAGATTTGAACT 1318–1331 1.000 74.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCATTTCCATCTCCGAGCAT TAATCAGGCGACACCCAGAT 1325–1338 1.000 74.3
trnC-GCA-petN_p1 trnC-GCA-petN ACAAAACAAGCAAAGGGGGA AGCCCAAGCGAGACTTACTA 850–888 1.000 82.3
trnC-GCA-petN_p2 trnC-GCA-petN TTGTATCCTTTTGGCGGCAT AGCCCAAGCGAGACTTACTA 815–853 1.000 82.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 779–817 1.000 80.9
trnC-GCA-petN_p4 trnC-GCA-petN ACAAAACAAGCAAAGGGGGA AGAGTCCACTTCTTCCCCAT 911–949 1.000 80.4
trnC-GCA-petN_p5 trnC-GCA-petN TTGTATCCTTTTGGCGGCAT AGAGTCCACTTCTTCCCCAT 876–914 1.000 80.4
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA ATCCACGGCTGAAACGTATC 617–748 1.000 86.5
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA AGTTGGATAGGATGGCCCTT 585–716 1.000 86.5
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATCCACGGCTGAAACGTATC 581–712 1.000 86.3
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA AGTTGGATAGGATGGCCCTT 549–680 1.000 86.3
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CTGGTAGAGCAGAGGACTGA ATCCACGGCTGAAACGTATC 605–736 1.000 85.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Boswellia bullata PQ586176.1 159212 View on NCBI ↗
Boswellia dioscoridis PQ586133.1 159192 View on NCBI ↗
Boswellia elongata PQ586177.1 159210 View on NCBI ↗
Boswellia frereana PQ586134.1 159215 View on NCBI ↗
Boswellia neglecta OQ730222.1 159216 View on NCBI ↗
Boswellia sacra NC_029420.1 160543 View on NCBI ↗
Boswellia serrata PQ594818.1 159519 View on NCBI ↗