Markers + reference

Burmeistera

17 species · Campanulaceae · Asterales

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Species 17
Genome length 164–166 kb
Candidate markers 279
Primer pairs 75

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 8 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK (UUU)-rps16 LSC 580 0.0117 1.00 60.0 yes View details
rps16-trnQ (UUG) LSC 1315 0.1499 0.80 76.5 yes View details
trnQ (UUG)-psbK LSC 719 0.0597 0.87 78.9 yes View details
rpoB-trnC (GCA) LSC 1948 0.0100 1.00 58.2 yes View details
ndhC-psaI LSC 1041 0.0213 1.00 64.7 yes View details
petA-psbJ LSC 973 0.0177 0.99 70.2 yes View details
ycf1 IRb 7236 0.0077 0.98 50.2 yes View details
ycf1 IRa 7236 0.0072 0.98 49.7 no View details
trnT (UGU)-trnL (UAA) LSC 677 0.0144 1.00 73.7 yes View details
rpl32-ndhF SSC 812 0.0103 1.00 64.6 yes View details
trnS (GCU)-trnG (UCC) LSC 720 0.0118 1.00 64.1 yes View details
ndhD-ccsA SSC 241 0.0205 1.00 62.4 yes View details
trnH (GUG)-psbA LSC 334 0.0128 1.00 60.4 yes View details
petG-trnW (CCA) LSC 101 0.0266 1.00 60.2 yes View details
psbE-petL LSC 1301 0.0087 0.99 60.1 yes View details
trnL (UAG)-rpl32 SSC 464 0.0132 0.98 59.8 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH (GUG)-psbA_p1 trnH (GUG)-psbA CAATCCACTGCCTTCATCCA CCGTGCTAACCTTGGTATGG 466–477 1.000 81.0
trnH (GUG)-psbA_p2 trnH (GUG)-psbA AATCCACTGCCTTCATCCAC CCGTGCTAACCTTGGTATGG 465–476 1.000 81.0
trnH (GUG)-psbA_p3 trnH (GUG)-psbA ACAATCCACTGCCTTCATCC CCGTGCTAACCTTGGTATGG 467–478 1.000 81.0
trnH (GUG)-psbA_p4 trnH (GUG)-psbA CAATCCACTGCCTTCATCCA ACCGTGCTAACCTTGGTATG 467–478 1.000 80.5
trnH (GUG)-psbA_p5 trnH (GUG)-psbA AATCCACTGCCTTCATCCAC ACCGTGCTAACCTTGGTATG 466–477 1.000 80.5
trnK (UUU)-rps16_p1 trnK (UUU)-rps16 TAAGAATGGGAGCTCGTTGC GCCCAAAAACCAAAAACCGA 1387–1452 1.000 90.8
trnK (UUU)-rps16_p2 trnK (UUU)-rps16 TAAGAATGGGAGCTCGTTGC CTCAATCCTCGGAACCTTGG 1366–1431 1.000 90.8
trnK (UUU)-rps16_p3 trnK (UUU)-rps16 TAAGAATGGGAGCTCGTTGC CGTTGCAATTGATGTTCGCT 1094–1135 0.941 85.3
trnK (UUU)-rps16_p4 trnK (UUU)-rps16 TAAGAATGGGAGCTCGTTGC CGCACTCTTCCAATAAGGCT 1569–1628 0.471 64.5
trnK (UUU)-rps16_p5 trnK (UUU)-rps16 TAAGAATGGGAGCTCGTTGC GAAAGGTGGCTCACTTCCAA 1477–1525 0.294 56.5
rps16-trnQ (UUG)_p1 rps16-trnQ (UUG) AGCGAACATCAATTGCAACG CCAAGATGACTTCATGCCGA 1953–2637 1.000 91.5
rps16-trnQ (UUG)_p2 rps16-trnQ (UUG) GCGAACATCAATTGCAACGA CCAAGATGACTTCATGCCGA 1952–2636 1.000 91.5
rps16-trnQ (UUG)_p3 rps16-trnQ (UUG) TTGCTTTCTACCACAGCGTT CCAAGATGACTTCATGCCGA 1916–2600 1.000 91.5
rps16-trnQ (UUG)_p4 rps16-trnQ (UUG) AGCGAACATCAATTGCAACG CTTACAGCAGCTTGCCAAAC 1674–2358 1.000 91.3
rps16-trnQ (UUG)_p5 rps16-trnQ (UUG) TGCTTTCTACCACAGCGTTT CCAAGATGACTTCATGCCGA 1915–2599 0.882 86.8
trnQ (UUG)-psbK_p1 trnQ (UUG)-psbK TTGGAAGTGAGCCACCTTTC CCAGGTCCGTGGAAAGAAAA 2290–2977 0.882 86.9
trnQ (UUG)-psbK_p2 trnQ (UUG)-psbK TTGGAAGTGAGCCACCTTTC CCAAGATGACTTCATGCCGA 1566–2253 0.882 86.9
trnQ (UUG)-psbK_p3 trnQ (UUG)-psbK TGCTTGTAGTCTTTCGGGTG CCAAGATGACTTCATGCCGA 1340–1824 0.824 83.4
trnQ (UUG)-psbK_p4 trnQ (UUG)-psbK CGGCAATACCCATAGCACAT CTTACAGCAGCTTGCCAAAC 784–1153 0.412 63.9
trnQ (UUG)-psbK_p5 trnQ (UUG)-psbK CGGCAATACCCATAGCACAT CCAAGATGACTTCATGCCGA 1063–1432 0.412 63.7
trnS (GCU)-trnG (UCC)_p1 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA AGGAGGTTCATAGAACGAATCAC 738–873 0.941 60.6
trnS (GCU)-trnG (UCC)_p2 trnS (GCU)-trnG (UCC) ACGAAAACGGAAAGAGAGGG AGGAGGTTCATAGAACGAATCAC 744–879 0.941 60.5
trnS (GCU)-trnG (UCC)_p3 trnS (GCU)-trnG (UCC) ACGGAAAGAGAGGGATTCGA GGAGGTTCATAGAACGAATCACA 737–872 0.941 58.7
trnS (GCU)-trnG (UCC)_p4 trnS (GCU)-trnG (UCC) ACGAAAACGGAAAGAGAGGG GGAGGTTCATAGAACGAATCACA 743–878 0.941 58.6
trnS (GCU)-trnG (UCC)_p5 trnS (GCU)-trnG (UCC) AGTCATCGACGAAAACGGAA AGGAGGTTCATAGAACGAATCAC 752–887 0.941 58.4
rpoB-trnC (GCA)_p1 rpoB-trnC (GCA) CCTGATCGATGAACCTGCAA GGTGCAGAGTCAAAAAGGGA 2299–2406 1.000 85.8
rpoB-trnC (GCA)_p2 rpoB-trnC (GCA) AGTCCCGCGGATACATAGAA GGTGCAGAGTCAAAAAGGGA 2468–2575 1.000 85.7
rpoB-trnC (GCA)_p3 rpoB-trnC (GCA) TAGACTCGACCCCATAGCTG GGTGCAGAGTCAAAAAGGGA 2784–2891 1.000 85.3
rpoB-trnC (GCA)_p4 rpoB-trnC (GCA) TCGACCCCATAGCTGATGAT GGTGCAGAGTCAAAAAGGGA 2779–2886 0.941 82.7
rpoB-trnC (GCA)_p5 rpoB-trnC (GCA) ATTGGATCCCCACCTACACA GGTGCAGAGTCAAAAAGGGA 2924–2993 0.765 74.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Burmeistera auriculata NC_035778.1 165772 View on NCBI ↗
Burmeistera borjensis NC_035777.1 163961 View on NCBI ↗
Burmeistera ceratocarpa NC_035776.1 165820 View on NCBI ↗
Burmeistera crispiloba NC_035775.1 165350 View on NCBI ↗
Burmeistera cyclostigmata NC_035774.1 165032 View on NCBI ↗
Burmeistera cylindrocarpa NC_035773.1 164865 View on NCBI ↗
Burmeistera domingensis NC_035772.1 165547 View on NCBI ↗
Burmeistera fuscoapicata NC_035771.1 165222 View on NCBI ↗
Burmeistera loejtnantii NC_035770.1 165888 View on NCBI ↗
Burmeistera lutosa NC_035769.1 165367 View on NCBI ↗
Burmeistera oyacachensis NC_035768.1 164048 View on NCBI ↗
Burmeistera parviflora NC_035767.1 164989 View on NCBI ↗
Burmeistera pirrensis NC_035766.1 165353 View on NCBI ↗
Burmeistera resupinata NC_035765.1 166128 View on NCBI ↗
Burmeistera rubrosepala NC_035764.1 165466 View on NCBI ↗
Burmeistera smaragdi NC_035763.1 165288 View on NCBI ↗
Burmeistera sodiroana NC_035762.1 165511 View on NCBI ↗