Markers + reference

Dianthus

28 species · Caryophyllaceae · Caryophyllales

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Species 28
Genome length 125–150 kb
Candidate markers 224
Primer pairs —

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 224 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG Genome 706 0.0086 1.00 51.2 no View details
trnM-CAU-atpE Genome 252 0.0351 0.98 72.4 no View details
rps18 Genome 312 0.0069 0.98 44.3 no View details
rpl16 Genome 1359 0.0078 0.98 60.3 no View details
rpl32-trnL-UAG Genome 734 0.0078 0.94 64.6 no View details
psaC Genome 246 0.0003 1.00 22.0 no View details
rps15-trnH-GUG Genome 3959 0.0065 1.00 64.7 no View details
ndhD-psaC Genome 127 0.0411 0.99 71.6 no View details
trnH-GUG-psbA Genome 210 0.0201 1.00 64.1 no View details
clpP Genome 2058 0.0035 1.00 62.2 no View details
psaA-ycf3 Genome 1082 0.0047 1.00 62.1 no View details
rpl20-rps12 Genome 797 0.0071 1.00 59.1 no View details
trnS-GCU-trnR-UCU Genome 1852 0.0037 0.97 58.0 no View details
petD Genome 1245 0.0040 0.99 57.9 no View details
rps4-trnT-UGU Genome 547 0.0082 0.95 57.4 no View details
trnE-UUC-trnT-GGU Genome 725 0.0088 0.96 57.3 no View details
psaC-ndhE Genome 409 0.0077 1.00 57.3 no 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.

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (28)

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

Species Accession Length (bp) Link
Dianthus alpinus OR915884.1 124939 View on NCBI ↗
Dianthus barbatus NC_082202.1 149660 View on NCBI ↗
Dianthus caryophyllus NC_039650.1 147604 View on NCBI ↗
Dianthus chinensis NC_053731.1 149570 View on NCBI ↗
Dianthus chinensis x Dianthus cincinnatus NC_082199.1 149192 View on NCBI ↗
Dianthus cincinnatus NC_082200.1 149800 View on NCBI ↗
Dianthus cintranus OR915886.1 124707 View on NCBI ↗
Dianthus fruticosus subsp. amorginus MT150102.1 149623 View on NCBI ↗
Dianthus fruticosus subsp. carpathus MT150103.1 149517 View on NCBI ↗
Dianthus fruticosus subsp. creticus MT150104.1 149611 View on NCBI ↗
Dianthus fruticosus subsp. fruticosus MT150105.1 149253 View on NCBI ↗
Dianthus fruticosus subsp. occidentalis MT150106.1 149494 View on NCBI ↗
Dianthus gratianopolitanus OR939661.1 124828 View on NCBI ↗
Dianthus helenae PZ251004.1 149567 View on NCBI ↗
Dianthus juniperinus subsp. aciphyllus MT150107.1 149607 View on NCBI ↗
Dianthus juniperinus subsp. bauhinorum MT150108.1 149475 View on NCBI ↗
Dianthus juniperinus subsp. heldreichii MT150109.1 149538 View on NCBI ↗
Dianthus juniperinus subsp. idaeus MT150110.1 149495 View on NCBI ↗
Dianthus juniperinus subsp. juniperinus MT150111.1 149541 View on NCBI ↗
Dianthus juniperinus subsp. kavusicus MT150112.1 149578 View on NCBI ↗
Dianthus longicalyx NC_050834.1 149596 View on NCBI ↗
Dianthus lumnitzeri OR939653.1 124715 View on NCBI ↗
Dianthus moravicus LN877396.1 149524 View on NCBI ↗
Dianthus petraeus OR915883.1 124839 View on NCBI ↗
Dianthus plumarius subsp. plumarius OR915887.1 124829 View on NCBI ↗
Dianthus serotinus OR939655.1 124820 View on NCBI ↗
Dianthus sternbergii OR915885.1 124767 View on NCBI ↗
Dianthus superbus NC_082201.1 149726 View on NCBI ↗