Markers + reference

Bruinsmia

2 species · Styracaceae · Ericales

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Species 2
Genome length 156–158 kb
Candidate markers 273
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnT-UGU-trnL-UAA LSC 790 0.0676 0.99 86.0 yes View details
rbcL-accD LSC 2611 0.1205 0.88 84.0 yes View details
rps12-psbB LSC 2232 0.0550 0.94 85.8 yes View details
trnN-GUU-ndhF IRb 1807 0.0602 0.95 89.6 yes View details
rps15-trnN-GUU SSC 6717 0.0407 0.98 77.6 yes View details
ndhI-ndhA SSC 100 0.0700 1.00 83.8 yes View details
atpB-rbcL LSC 443 0.0442 0.97 83.6 yes View details
rpl2-trnH-GUG LSC 77 0.1400 0.65 74.0 no View details
atpH-atpF LSC 367 0.0436 1.00 73.1 yes View details
trnL-UAG-ccsA SSC 112 0.1161 1.00 73.0 yes View details
rps19-rpl12 LSC 67 0.1642 1.00 72.5 yes View details
trnS-UGA LSC 89 0.0337 1.00 69.0 yes View details
petA-psbJ LSC 1045 0.0117 0.90 68.8 yes View details
trnF-GAA LSC 73 0.0548 1.00 67.6 yes View details
infA-rps8 LSC 121 0.0579 1.00 67.5 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpH-atpF_p1 atpH-atpF GGCTGGTTGTAGCATTAGCA CCAGTAGCCCAAAGAAACGA 456–471 1.000 79.3
atpH-atpF_p2 atpH-atpF TGGGCTGGTTGTAGCATTAG CCAGTAGCCCAAAGAAACGA 458–473 1.000 78.0
atpH-atpF_p3 atpH-atpF GGCTGGTTGTAGCATTAGCA TATTAAGCCCGAAACTCCCG 484–499 1.000 75.7
atpH-atpF_p4 atpH-atpF CGGAGGGAAAAATACGAGGT CCAGTAGCCCAAAGAAACGA 522–537 1.000 75.5
atpH-atpF_p5 atpH-atpF GCGGAGGGAAAAATACGAGG CCAGTAGCCCAAAGAAACGA 523–538 1.000 75.4
trnS-UGA_p1 trnS-UGA TTTTCTGGCTTGGCTAGGTG TCGACCTCTAGATTCACACCT 298 1.000 69.4
trnS-UGA_p2 trnS-UGA GATAGCCGAGCCATTTTCCT TCGACCTCTAGATTCACACCT 277 1.000 68.1
trnS-UGA_p3 trnS-UGA CCGGTCCGGTAAAAACCAAT TCGACCTCTAGATTCACACCT 245 1.000 66.7
trnS-UGA_p4 trnS-UGA TAGCCGAGCCATTTTCCTTT TCGACCTCTAGATTCACACCT 275 1.000 66.2
trnS-UGA_p5 trnS-UGA TTTTCTGGCTTGGCTAGGTG CGATAGGGGTGGTATTCACT 264 1.000 65.1
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 840–866 1.000 84.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 848–874 1.000 83.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 872–898 1.000 83.4
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 880–906 1.000 82.8
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 854–880 1.000 82.5
trnF-GAA_p1 trnF-GAA ACGACCCCAATCTGTATCCT TTGTCTTATGGTACGCGTGG 1345–1355 1.000 80.8
trnF-GAA_p2 trnF-GAA ACGACCCCAATCTGTATCCT AGTCATGTGGGAGGGAATGA 1170–1179 1.000 80.7
trnF-GAA_p3 trnF-GAA ACGACCCCAATCTGTATCCT AGAAAGTCATGTGGGAGGGA 1174–1183 1.000 80.5
trnF-GAA_p4 trnF-GAA TGACTGTGTCGGTAGAGGAA TTGTCTTATGGTACGCGTGG 1445–1455 1.000 79.9
trnF-GAA_p5 trnF-GAA ACGACCCCAATCTGTATCCT GCGTGGTCCAACAACAAAAA 1341 0.500 58.6
atpB-rbcL_p1 atpB-rbcL AACGATAAGCCCCGGTTTTT CACCAGCTTTGAATCCAACAC 564–912 1.000 74.6
atpB-rbcL_p2 atpB-rbcL AACGATAAGCCCCGGTTTTT ACCAGCTTTGAATCCAACACT 563–911 1.000 74.4
atpB-rbcL_p3 atpB-rbcL GGCGGAAAGGCTACATCTAG CACCAGCTTTGAATCCAACAC 602–950 1.000 73.9
atpB-rbcL_p4 atpB-rbcL GGCGGAAAGGCTACATCTAG ACCAGCTTTGAATCCAACACT 601–949 1.000 73.6
atpB-rbcL_p5 atpB-rbcL ATTTGAACGATAAGCCCCGG CACCAGCTTTGAATCCAACAC 569–917 1.000 72.7
rbcL-accD_p1 rbcL-accD GAGGCTAGCAAATGGAGTCC AGCATACTCGATCAAACGGG 2757–2914 1.000 89.8
rbcL-accD_p2 rbcL-accD AATGAGGGACGTGATCTTGC AGCATACTCGATCAAACGGG 2802–2959 1.000 89.7
rbcL-accD_p3 rbcL-accD GCTGCTTGTGAGGTATGGAA AGCATACTCGATCAAACGGG 2727–2884 1.000 89.2
rbcL-accD_p4 rbcL-accD AATGAGGGACGTGATCTTGC ATAACCCCAATTGCTACGGG 2729–2886 1.000 88.9
rbcL-accD_p5 rbcL-accD TGATCTTGCTCGTGAGGGTA AGCATACTCGATCAAACGGG 2791–2948 1.000 88.8

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
Bruinsmia polysperma NC_030180.1 157879 View on NCBI ↗
Bruinsmia styracoides NC_041137.1 156434 View on NCBI ↗