Markers + reference

Anatherum

25 species · Poaceae · Poales

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Species 25
Genome length 139–141 kb
Candidate markers 265
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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnT-GGU LSC 1780 0.0055 1.00 55.5 yes View details
trnT-GGU-trnE-UUC LSC 533 0.0194 0.97 58.2 yes View details
rpoC2 LSC 4440 0.0024 1.00 41.4 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0053 0.98 54.4 yes View details
petL-petG LSC 171 0.0284 1.00 56.8 yes View details
rps18 LSC 450 0.0038 1.00 36.2 yes View details
rpoA LSC 1020 0.0014 1.00 30.8 yes View details
rpl16 LSC 1473 0.0040 1.00 49.6 yes View details
rpl32-trnL-UAG SSC 552 0.0099 0.96 49.8 yes View details
rps16-trnQ-UUG LSC 1522 0.0036 1.00 58.3 yes View details
trnF-GAA-ndhJ LSC 591 0.0078 1.00 56.3 yes View details
trnD-GUC-psbM LSC 1074 0.0019 1.00 54.8 yes View details
trnN-GUU-rps15 IRb 1595 0.0011 1.00 54.5 yes View details
ndhF-rpl32 SSC 864 0.0036 1.00 53.8 yes View details
rps15-trnN-GUU IRa 1595 0.0011 1.00 53.6 yes View details
trnK-UUU-rps16 LSC 556 0.0054 0.99 52.5 yes View details
ndhC-trnV-UAC LSC 935 0.0031 0.97 52.2 yes View details
atpI-atpH LSC 835 0.0015 1.00 51.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACA 677–723 1.000 71.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CATAGCCGCACTTAAAAGCC GGTGCTCAACCTACAAGAACA 682–728 1.000 70.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAAC 677–723 1.000 67.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACA 676–722 1.000 67.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTACCAAGAGTCTGGACGA GGTGCTCAACCTACAAGAACA 733–779 1.000 66.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1215–1636 1.000 83.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1226–1647 1.000 83.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1219–1640 1.000 82.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1230–1651 1.000 82.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1221–1642 1.000 81.0
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 1900–2133 1.000 43.9
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1870–2103 1.000 43.7
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTCTGTCTTACCAAGGCA 1928–2161 1.000 43.4
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTCTGTCTTACCAAGGC 1929–2162 1.000 43.4
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1866–2099 1.000 43.0
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 598–659 1.000 76.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GAGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 577–638 1.000 75.9
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 597–658 1.000 74.2
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 560–621 1.000 74.2
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 576–637 1.000 74.1
trnD-GUC-psbM_p1 trnD-GUC-psbM AGAATAGGCACGCCATACAC GGCAGTAGGAACTAGAATGAACA 853–1250 0.960 56.6
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG GGCAGTAGGAACTAGAATGAACA 817–1214 1.000 56.5
trnD-GUC-psbM_p3 trnD-GUC-psbM AGAATAGGCACGCCATACAC AGGCAGTAGGAACTAGAATGAAC 854–1251 0.960 54.5
trnD-GUC-psbM_p4 trnD-GUC-psbM AGAATAGGCACGCCATACAC AGGCAGTAGGAACTAGAATGA 854–1251 0.960 53.2
trnD-GUC-psbM_p5 trnD-GUC-psbM AGAATAGGCACGCCATACAC TGCGAGAATATTGACTTCCA 814–1211 0.960 53.1
rpoC2_p1 rpoC2 CAGGAATTGTTAAATTTAGATATAGGA ATATTCGCCCTCTCCCTCTC 113–230 1.000 50.7
rpoC2_p2 rpoC2 TCAGGAATTGTTAAATTTAGATATAGG ATATTCGCCCTCTCCCTCTC 114–231 1.000 50.7
rpoC2_p3 rpoC2 AGGAATTGTTAAATTTAGATATAGGAC ATATTCGCCCTCTCCCTCTC 112–229 1.000 50.7
rpoC2_p4 rpoC2 CAGGAATTGTTAAATTTAGATATAGGA TTCATATTCGCCCTCTCCCT 149–233 0.960 44.9
rpoC2_p5 rpoC2 TCAGGAATTGTTAAATTTAGATATAGG TTCATATTCGCCCTCTCCCT 150–234 0.960 44.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (25)

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

Species Accession Length (bp) Link
Anatherum aequatoriensis MH181218.1 140088 View on NCBI ↗
Anatherum africanum NC_086835.1 140058 View on NCBI ↗
Anatherum arenarium NC_086836.1 140298 View on NCBI ↗
Anatherum bicorne NC_086834.1 140276 View on NCBI ↗
Anatherum brachystachyum NC_086838.1 140788 View on NCBI ↗
Anatherum capillipes NC_086837.1 140587 View on NCBI ↗
Anatherum eucomum subsp. huillense MH181180.1 139492 View on NCBI ↗
Anatherum floridanum MH181221.1 140528 View on NCBI ↗
Anatherum glaucescens MH181185.1 140278 View on NCBI ↗
Anatherum glaucophyllum OQ439993.1 140342 View on NCBI ↗
Anatherum glomeratum NC_086839.1 140571 View on NCBI ↗
Anatherum gyrans MH181171.1 140726 View on NCBI ↗
Anatherum ibityense NC_086840.1 140787 View on NCBI ↗
Anatherum insolitum MH181163.1 140278 View on NCBI ↗
Anatherum ivohibense OQ439998.1 140653 View on NCBI ↗
Anatherum laterale OQ440000.1 140384 View on NCBI ↗
Anatherum leucostachyum OQ439999.1 140343 View on NCBI ↗
Anatherum liebmannii MH181232.1 140695 View on NCBI ↗
Anatherum ligulatum MH181204.1 140511 View on NCBI ↗
Anatherum macrothrix OQ440002.1 140731 View on NCBI ↗
Anatherum pringlei NC_087662.1 139711 View on NCBI ↗
Anatherum selloanum MH181213.1 140651 View on NCBI ↗
Anatherum trichozygum NC_086843.1 140745 View on NCBI ↗
Anatherum urbanianum MH181230.1 140616 View on NCBI ↗
Anatherum virginicum NC_086842.1 140745 View on NCBI ↗