Markers + reference

Rhinanthus

3 species · Orobanchaceae · Lamiales

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Species 3
Genome length 145–145 kb
Candidate markers 267
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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 491 0.0027 1.00 44.0 yes View details
rpoC1 LSC 2805 0.0005 1.00 44.6 yes View details
atpB-rbcL LSC 760 0.0026 1.00 47.9 yes View details
clpP1 LSC 1946 0.0017 1.00 45.8 yes View details
psbB-psbT LSC 183 0.0000 1.00 29.6 yes View details
petD-rpoA LSC 356 0.0075 1.00 31.8 yes View details
rpl16 LSC 1273 0.0018 1.00 49.9 yes View details
ycf1 IRb 1665 0.0032 1.00 60.4 yes View details
ycf1 SSC 5370 0.0010 1.00 53.1 no View details
psbT-psbN LSC 61 0.0328 1.00 60.9 yes View details
rpl32-trnL-UAG SSC 761 0.0026 1.00 60.4 yes View details
ndhC-trnV-UAC LSC 1218 0.0011 1.00 60.2 yes View details
accD-psaI LSC 631 0.0021 1.00 60.1 yes View details
trnT-UGU-trnL-UAA LSC 735 0.0018 1.00 59.9 yes View details
psbA LSC 1059 0.0013 1.00 59.6 yes View details
ccsA SSC 960 0.0014 1.00 59.6 yes View details
rps16 LSC 1074 0.0012 1.00 59.5 yes View details
psbB LSC 1527 0.0013 1.00 59.5 yes View details
ycf3 LSC 1922 0.0010 1.00 58.7 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 555–557 1.000 79.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTGGCTGCTAT 569–571 1.000 79.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTGGCTGCTAT 568–570 1.000 79.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTGGCTGCTAT 570–572 1.000 79.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 610–612 1.000 77.8
psbA_p1 psbA TAAAGGAGCAATAACCCCGC ATTCGTTTGCTTGGGAGTCC 1210 1.000 76.0
psbA_p2 psbA TAACCCCGCTTGATAGACCA ATTCGTTTGCTTGGGAGTCC 1199 1.000 75.4
psbA_p3 psbA GAGCAATAACCCCGCTTGAT ATTCGTTTGCTTGGGAGTCC 1205 1.000 73.9
psbA_p4 psbA TAAAGGAGCAATAACCCCGC TTTGCTTGGGAGTCCCTGAT 1205 1.000 72.4
psbA_p5 psbA TAACCCCGCTTGATAGACCA TTTGCTTGGGAGTCCCTGAT 1194 1.000 71.7
rps16_p1 rps16 ACAGCAGAAAATAAAGGGGG AATTCCACACCGGTTCCAAA 1208 1.000 60.2
rps16_p2 rps16 ACAGCAGAAAATAAAGGGGG TTCCACACCGGTTCCAAATT 1206 1.000 60.2
rps16_p3 rps16 ACAGCAGAAAATAAAGGGGG ATCAATTCCACACCGGTTCC 1211 1.000 59.5
rps16_p4 rps16 ACAGCAGAAAATAAAGGGGG ATTCCACACCGGTTCCAAAT 1207 1.000 58.4
rps16_p5 rps16 ACAGCAGAAAATAAAGGGGG CGACAGCCGAATGAATGACT 1251 1.000 58.0
rpoC1_p1 rpoC1 CGGAATTCCTACTGGTATCGT AGGAAGGAAGCTTAATCGGA 2884 1.000 47.5
rpoC1_p2 rpoC1 AGAGATCGGAATTCCTACTGGT AGGAAGGAAGCTTAATCGGA 2890 1.000 46.8
rpoC1_p3 rpoC1 CGGAATTCCTACTGGTATCGT AGGAAGGAAGCTTAATCGGAA 2884 1.000 45.8
rpoC1_p4 rpoC1 TCGGAATTCCTACTGGTATCG AGGAAGGAAGCTTAATCGGA 2885 1.000 45.3
rpoC1_p5 rpoC1 AGAGATCGGAATTCCTACTGGT AGGAAGGAAGCTTAATCGGAA 2890 1.000 45.1
ycf3_p1 ycf3 TGGTGCGTCCAAACCAAAAA TAGAATGGAGGTGGCTAGCT 2043–2047 1.000 67.5
ycf3_p2 ycf3 TGGTGCGTCCAAACCAAAAA GATCATTTTCCCGCGAGAGG 2078–2082 1.000 65.1
ycf3_p3 ycf3 TGGTGCGTCCAAACCAAAAA GGATCATTTTCCCGCGAGAG 2079–2083 1.000 65.1
ycf3_p4 ycf3 TGGTGCGTCCAAACCAAAA TAGAATGGAGGTGGCTAGCT 2043–2047 1.000 65.0
ycf3_p5 ycf3 TGGTGCGTCCAAACCAAAAA GCGAGAGGGAATGAGAAGAA 2066–2070 1.000 63.6
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 797 1.000 77.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA TAGGAAAAAGCCGGCTATCG CCGTAGCGTCTACCGATTTC 848 1.000 76.3
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 829 1.000 76.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 791 1.000 75.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GGTTTCCATACCAAGGCTCA 829 1.000 75.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Rhinanthus alectorolophus subsp. alectorolophus PP541885.1 145309 View on NCBI ↗
Rhinanthus freynii PP541886.1 145369 View on NCBI ↗
Rhinanthus minor PP541887.1 145323 View on NCBI ↗