Markers + reference

Brandisia

11 species · Orobanchaceae · Lamiales

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Species 11
Genome length 155–155 kb
Candidate markers 277
Primer pairs 90

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 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 568 0.0341 0.96 74.1 yes View details
trnS-GCU-trnG-UCC LSC 682 0.0089 0.99 47.3 yes View details
petA-psbJ LSC 1048 0.0106 1.00 62.4 yes View details
psbE-petL LSC 904 0.0127 1.00 56.6 yes View details
ndhF SSC 2265 0.0075 1.00 44.2 yes View details
ndhF-rpl32 SSC 464 0.0114 0.99 52.9 yes View details
rpl32-trnL-UAG SSC 812 0.0149 0.98 65.1 yes View details
ndhA SSC 2167 0.0088 1.00 48.5 yes View details
ycf1 SSC 5592 0.0099 1.00 42.9 yes View details
atpA-atpF LSC 82 0.0477 0.99 68.0 yes View details
psbT-psbN LSC 60 0.0558 1.00 65.0 yes View details
trnT-GGU-psbD LSC 1310 0.0066 0.99 60.5 yes View details
psaB-psaA LSC 25 0.0335 1.00 58.8 yes View details
rpl22 LSC 471 0.0130 1.00 58.8 yes View details
ndhC-trnV-UAC LSC 1158 0.0090 0.98 58.5 yes View details
trnM-CAU-atpE LSC 210 0.0124 1.00 58.4 yes View details
atpF-atpH LSC 380 0.0082 1.00 57.5 yes View details
psbB-psbT LSC 193 0.0176 1.00 57.0 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTGGCTGCTAT 562–648 1.000 90.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTGGCTGCTAT 576–662 1.000 90.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTGGCTGCTAT 575–661 1.000 90.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTGGCTGCTAT 577–663 1.000 90.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TAGACCTGGCTGCTATCGAA 558–644 0.909 84.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 751–766 1.000 54.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 750–765 1.000 54.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 754–769 1.000 53.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 753–768 1.000 53.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 752–767 1.000 53.4
atpA-atpF_p1 atpA-atpF AATTTCGTCGGCTCGAATGG TTAGCATGTTGGGAGCGATG 138–179 1.000 80.4
atpA-atpF_p2 atpA-atpF AATTTCGTCGGCTCGAATGG TGTTGGGAGCGATGAAAGAA 132–173 1.000 78.9
atpA-atpF_p3 atpA-atpF GTCGGCTCGAATGGTTACC TTAGCATGTTGGGAGCGATG 132–173 1.000 78.0
atpA-atpF_p4 atpA-atpF AATTTCGTCGGCTCGAATGG ATTAGCATGTTGGGAGCGAT 139–180 1.000 77.8
atpA-atpF_p5 atpA-atpF ATTTCGTCGGCTCGAATGG TTAGCATGTTGGGAGCGATG 137–178 1.000 77.8
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA CCTGAGGCAGAGGGAAAAAT 532–546 1.000 80.1
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG CCTGAGGCAGAGGGAAAAAT 533–547 1.000 79.5
atpF-atpH_p3 atpF-atpH AGTGGCCCAAAGAAACGAAA CCTGAGGCAGAGGGAAAAAT 534–548 1.000 78.7
atpF-atpH_p4 atpF-atpH TTAAATCCGAAACTCCCGGC CCTGAGGCAGAGGGAAAAAT 562–576 1.000 78.3
atpF-atpH_p5 atpF-atpH TGGCCCAAAGAAACGAAAGA GCAGAGGGAAAAATACGAGGT 526–540 1.000 76.1
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CCGCAACCAGTCATCCATAA 1448–1460 1.000 82.2
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGACCAGCCTACAAAAACGA 1478–1490 1.000 81.6
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA CCGCAACCAGTCATCCATAA 1411–1423 1.000 80.9
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1468–1480 1.000 80.5
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1441–1453 1.000 80.2
psaB-psaA_p1 psaB-psaA AACCCTTGGCTAAACCTTGG GTACAAGGACGTGCTGTAGG 156 1.000 81.4
psaB-psaA_p2 psaB-psaA AACCCTTGGCTAAACCTTGG ACAACATGGGCGTTCTTCTT 105 1.000 81.3
psaB-psaA_p3 psaB-psaA AACCCTTGGCTAAACCTTGG TACAAGGACGTGCTGTAGGA 155 1.000 80.8
psaB-psaA_p4 psaB-psaA AACCCTTGGCTAAACCTTGG GGGCGTTCTTCTTAGCAAGA 98 1.000 80.8
psaB-psaA_p5 psaB-psaA AATACGACGAGTAGTGGGGT GTACAAGGACGTGCTGTAGG 184 1.000 80.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Brandisia cauliflora NC_073570.1 154662 View on NCBI ↗
Brandisia chevalieri NC_077467.1 155069 View on NCBI ↗
Brandisia discolor NC_077468.1 155232 View on NCBI ↗
Brandisia glabrescens NC_077469.1 155207 View on NCBI ↗
Brandisia hancei NC_077470.1 155223 View on NCBI ↗
Brandisia hancei x Brandisia discolor NC_077474.1 155232 View on NCBI ↗
Brandisia kwangsiensis NC_077471.1 155029 View on NCBI ↗
Brandisia racemosa NC_077472.1 154832 View on NCBI ↗
Brandisia rosea var. flava OP262739.1 155112 View on NCBI ↗
Brandisia scandens NC_077473.1 155086 View on NCBI ↗
Brandisia swinglei NC_042954.1 155344 View on NCBI ↗