Markers + reference

Brachypodium

3 species · Poaceae · Poales

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Species 3
Genome length 136–137 kb
Candidate markers 265
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-trnI Genome 541 0.0240 0.98 61.0 yes View details
psbM-petN Genome 845 0.0161 0.93 66.2 yes View details
trnL-trnF Genome 364 0.0256 0.93 53.2 yes View details
rbcL-rpl23 Genome 325 0.0168 0.98 51.7 yes View details
rpl23-psaI Genome 1075 0.0164 0.98 57.8 yes View details
petA-psbJ Genome 840 0.0199 1.00 66.4 yes View details
ndhF Genome 2211 0.0155 1.00 52.2 yes View details
ndhF-rpl32 Genome 878 0.0263 0.95 65.3 yes View details
rpl32-trnL Genome 701 0.0394 0.99 70.5 yes View details
ndhA Genome 2136 0.0125 1.00 51.3 yes View details
psbT-psbN Genome 48 0.0833 1.00 86.7 yes View details
ndhC-trnV Genome 899 0.0155 0.98 66.1 yes View details
ycf4-cemA Genome 429 0.0205 0.99 64.1 yes View details
trnD-psbM Genome 796 0.0127 0.99 63.4 yes View details
petN-trnC Genome 935 0.0146 1.00 63.1 yes View details
atpI-atpH Genome 380 0.0140 1.00 63.1 yes View details
trnG-trnfM Genome 434 0.0200 1.00 61.6 yes View details
rps16-trnQ Genome 630 0.0149 1.00 61.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 703–839 1.000 80.0
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 714–850 1.000 79.5
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA AGTGTCGCATAAAACCCGAA 772–908 1.000 79.1
rps16-trnQ_p4 rps16-trnQ AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 707–843 1.000 78.9
rps16-trnQ_p5 rps16-trnQ TCATGTCCTTCAAGTCGCAC AGTGTCGCATAAAACCCGAA 783–919 1.000 78.5
trnG-trnfM_p1 trnG-trnfM GTCGACCCAAGCGGATATAC CGAGGCTCATAACCTTGAGG 590–592 1.000 79.7
trnG-trnfM_p2 trnG-trnfM GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 550–552 1.000 79.7
trnG-trnfM_p3 trnG-trnfM GTCGACCCAAGCGGATATAC CAGTTTGGTAGCTCACGAGG 605–607 1.000 79.2
trnG-trnfM_p4 trnG-trnfM GCGAGCGTAGTTCAATGGTA CAGTTTGGTAGCTCACGAGG 565–567 1.000 79.2
trnG-trnfM_p5 trnG-trnfM CGTAGCGAGCGTAGTTCAAT CGAGGCTCATAACCTTGAGG 554–556 1.000 78.9
trnG-trnI_p1 trnG-trnI CATCGTTAGCTTGGAAGGCT GAACCGATGACTTACGCCTT 1793–1826 1.000 83.1
trnG-trnI_p2 trnG-trnI CGTTAGCTTGGAAGGCTAGG GAACCGATGACTTACGCCTT 1790–1823 1.000 82.9
trnG-trnI_p3 trnG-trnI CCGAGCTGGAACAATATGCT GAACCGATGACTTACGCCTT 1503–1521 1.000 82.7
trnG-trnI_p4 trnG-trnI CATCGTTAGCTTGGAAGGCT CCGATGACTTACGCCTTACC 1790–1823 1.000 81.9
trnG-trnI_p5 trnG-trnI CTTCGCGACTCTGTACTCAG GAACCGATGACTTACGCCTT 1330 0.333 52.0
trnD-psbM_p1 trnD-psbM TTCAATTGGTCAGAGCACCG TGCAGTAGCGATAAATGCGA 888–896 1.000 76.7
trnD-psbM_p2 trnD-psbM TTCAATTGGTCAGAGCACCG GTGCAGTAGCGATAAATGCG 889–897 1.000 76.1
trnD-psbM_p3 trnD-psbM TAGGTATGCCATACACCCCG TGCAGTAGCGATAAATGCGA 920–928 1.000 75.2
trnD-psbM_p4 trnD-psbM TTCAATTGGTCAGAGCACCG AATGAACAGTGCAGTAGCGA 897–905 1.000 74.8
trnD-psbM_p5 trnD-psbM TAGGTATGCCATACACCCCG GTGCAGTAGCGATAAATGCG 921–929 1.000 74.6
psbM-petN_p1 psbM-petN TCGCATTTATCGCTACTGCA TCTTGCTTGGGCTGCTTTAA 935–1010 1.000 83.7
psbM-petN_p2 psbM-petN CGCATTTATCGCTACTGCAC TCTTGCTTGGGCTGCTTTAA 934–1009 1.000 83.1
psbM-petN_p3 psbM-petN TCGCATTTATCGCTACTGCA CTTTCACTAGTGGTGTGGGG 895–970 1.000 82.3
psbM-petN_p4 psbM-petN TCGCATTTATCGCTACTGCA AGTAAGTCTTGCTTGGGCTG 941–1016 1.000 82.2
psbM-petN_p5 psbM-petN TCGCTACTGCACTGTTCATT TCTTGCTTGGGCTGCTTTAA 926–1001 1.000 81.8
petN-trnC_p1 petN-trnC TTAAAGCAGCCCAAGCAAGA ACGTGGGTGAATACTTGCTC 1087–1088 1.000 80.7
petN-trnC_p2 petN-trnC CAGCCCAAGCAAGACTTACT ACGTGGGTGAATACTTGCTC 1081–1082 1.000 79.2
petN-trnC_p3 petN-trnC TTAAAGCAGCCCAAGCAAGA CGTGGGTGAATACTTGCTCT 1086–1087 1.000 78.3
petN-trnC_p4 petN-trnC TTAAAGCAGCCCAAGCAAGA AACGTGGGTGAATACTTGCT 1088–1089 1.000 76.9
petN-trnC_p5 petN-trnC CAGCCCAAGCAAGACTTACT CGTGGGTGAATACTTGCTCT 1080–1081 1.000 76.9

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
Brachypodium hybridum NC_036836.1 136327 View on NCBI ↗
Brachypodium pinnatum NC_059961.1 136568 View on NCBI ↗
Brachypodium sylvaticum NC_058601.1 136392 View on NCBI ↗