Markers + reference

Brownlowia

2 species · Malvaceae · Malvales

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Species 2
Genome length 159–160 kb
Candidate markers 267
Primer pairs 85

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 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 4074 0.0002 1.00 54.1 yes View details
petN-psbM LSC 1148 0.0000 1.00 45.2 yes View details
rps14 LSC 303 0.0000 1.00 23.7 yes View details
ycf3 LSC 2030 0.0010 1.00 52.3 yes View details
ycf3-trnS-GGA LSC 959 0.0010 1.00 59.3 yes View details
trnM-CAU-atpE LSC 238 0.0042 1.00 54.9 yes View details
clpP1-psbB LSC 409 0.0000 1.00 25.0 yes View details
psbB LSC 1527 0.0007 1.00 59.1 yes View details
rpl16 LSC 1558 0.0006 1.00 59.0 yes View details
rps14-psaB LSC 128 0.0394 0.99 75.9 yes View details
petA-psbJ LSC 1012 0.0000 0.98 60.6 yes View details
rpl32-trnL-UAG SSC 1122 0.0009 1.00 59.3 yes View details
atpF-atpH LSC 632 0.0000 1.00 59.1 yes View details
ndhC-trnV-UAC LSC 1125 0.0000 1.00 58.8 yes View details
ndhF-rpl32 SSC 1021 0.0000 1.00 58.8 yes View details
psbM LSC 105 0.0095 1.00 58.0 yes View details
clpP1 LSC 2130 0.0000 1.00 57.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA TGGTTGTAGCATTGGCACTT 715–717 1.000 79.9
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGTTGTAGCATTGGCACTT 743–745 1.000 79.2
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA CTGGTTGTAGCATTGGCACT 716–718 1.000 76.2
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA ATGGGCTGGTTGTAGCATTG 721–723 1.000 75.7
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CTGGTTGTAGCATTGGCACT 744–746 1.000 75.6
rpoC2_p1 rpoC2 CGCGAATCTCAGCAATCACT TTACAGGGGGTACTGCAGAA 243 1.000 74.3
rpoC2_p2 rpoC2 CGCGAATCTCAGCAATCACT TTTACAGGGGGTACTGCAGA 244 1.000 74.3
rpoC2_p3 rpoC2 CGCGAATCTCAGCAATCACT GAACATGTACGAGCCCCTTT 226 1.000 73.8
rpoC2_p4 rpoC2 CGCGAATCTCAGCAATCACT CATTGGAGAACCGGGAACTC 299 1.000 72.5
rpoC2_p5 rpoC2 CGCGAATCTCAGCAATCACT AACTTTTCATACCGGCGGAG 266 1.000 72.5
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGTACAAGGAAGGCGGTAGA 1637–1641 1.000 79.6
petN-psbM_p2 petN-psbM TAGTGGAAGGGAAGCAGTCA TGTACAAGGAAGGCGGTAGA 2059–2063 1.000 79.4
petN-psbM_p3 petN-psbM AGTAGTGGAAGGGAAGCAGT TGTACAAGGAAGGCGGTAGA 2061–2065 1.000 79.4
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGATTGTACAAGGAAGGCGG 1641–1645 1.000 79.3
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA GATTGTACAAGGAAGGCGGT 1640–1644 1.000 79.3
psbM_p1 psbM ACTGCTGATTCTAGTCCATTCA ATCCCGAGTTATTGCGAAGT 236 1.000 47.7
psbM_p2 psbM GGATACTGCTGATTCTAGTCCA ATCCCGAGTTATTGCGAAGT 240 1.000 46.8
psbM_p3 psbM AGACGTGAAATTGGAATCCT ATCCCGAGTTATTGCGAAGT 205 1.000 45.7
psbM_p4 psbM ACTGCTGATTCTAGTCCATTCA AATCCCGAGTTATTGCGAAGT 237 1.000 45.4
psbM_p5 psbM GGATACTGCTGATTCTAGTCCA AATCCCGAGTTATTGCGAAGT 241 1.000 44.5
rps14_p1 rps14 GCGCCCCTCTTCCATATATG ACATCTAGGATCCGACTTGT 471 1.000 58.6
rps14_p2 rps14 ATGCGCCCCTCTTCCATATA ACATCTAGGATCCGACTTGT 473 1.000 56.1
rps14_p3 rps14 TGCGCCCCTCTTCCATATAT ACATCTAGGATCCGACTTGT 472 1.000 56.1
rps14_p4 rps14 GCGCCCCTCTTCCATATATG TCTACATCTAGGATCCGACTTGT 474 1.000 55.4
rps14_p5 rps14 GGCCCCTCTATGATCATCGA ACATCTAGGATCCGACTTGT 413 1.000 55.4
rps14-psaB_p1 rps14-psaB TTCTCACTCAACGACGGAAC ACCAGTGGCTCTTTCCATTG 364–365 1.000 79.6
rps14-psaB_p2 rps14-psaB TTCTCACTCAACGACGGAAC CCAGTGGCTCTTTCCATTGT 363–364 1.000 79.6
rps14-psaB_p3 rps14-psaB CTCACTCAACGACGGAACTT ACCAGTGGCTCTTTCCATTG 362–363 1.000 79.6
rps14-psaB_p4 rps14-psaB CTCACTCAACGACGGAACTT CCAGTGGCTCTTTCCATTGT 361–362 1.000 79.6
rps14-psaB_p5 rps14-psaB TTCTCACTCAACGACGGAAC GCTCTTTCCATTGTGCAAGC 357–358 1.000 78.0

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
Brownlowia argentata PP419969.1 159510 View on NCBI ↗
Brownlowia tersa PP419968.1 159478 View on NCBI ↗