Markers + reference

Cerastium

6 species · Caryophyllaceae · Caryophyllales

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Species 6
Genome length 148–149 kb
Candidate markers 267
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 776 0.0180 0.99 67.9 yes View details
psbM-trnD-GUC LSC 558 0.0226 1.00 57.5 yes View details
trnD-GUC-trnY-GUA LSC 378 0.0198 1.00 61.3 yes View details
psaA-ycf3 LSC 827 0.0140 0.99 62.0 yes View details
rps4-trnT-UGU LSC 352 0.0095 1.00 46.7 yes View details
trnT-UGU-trnL-UAA LSC 649 0.0159 0.95 70.3 yes View details
ndhC-trnV-UAC LSC 1136 0.0142 1.00 62.8 yes View details
petA-psbJ LSC 900 0.0131 1.00 63.9 yes View details
psbE-petL LSC 1172 0.0103 0.99 59.9 yes View details
psaJ-rpl33 LSC 430 0.0257 1.00 59.3 yes View details
rpl16 LSC 1270 0.0094 1.00 49.7 yes View details
ndhB-rps7 IRa 228 0.0053 0.62 62.7 no View details
rpl20-rps12 LSC 768 0.0084 1.00 61.6 yes View details
trnH-GUG-psbA LSC 197 0.0233 1.00 60.8 yes View details
trnR-UCU-atpA LSC 119 0.0303 1.00 60.4 yes View details
petG-trnW-CCA LSC 122 0.0219 1.00 59.8 yes View details
trnT-GGU-psbD LSC 1082 0.0096 1.00 59.6 yes View details
psbI-trnS-GCU LSC 178 0.0187 1.00 58.1 yes View details
trnL-UAA-trnF-GAA LSC 375 0.0162 1.00 56.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 255–269 1.000 86.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 269–283 1.000 85.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 268–282 1.000 85.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 270–284 1.000 85.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 304–318 1.000 83.3
psbI-trnS-GCU_p1 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT AAGAGGGAGAGATGGCTGAG 305–317 1.000 79.1
psbI-trnS-GCU_p2 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TTCAAGAGGGAGAGATGGCT 308–320 1.000 78.6
psbI-trnS-GCU_p3 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT CGAGTTATTCGTACCGAGGG 252–264 1.000 78.2
psbI-trnS-GCU_p4 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT CAAGAGGGAGAGATGGCTGA 306–318 1.000 76.7
psbI-trnS-GCU_p5 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TCAAGAGGGAGAGATGGCTG 307–319 1.000 76.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG ACGAATCACACTTTTACCACT 871–900 1.000 58.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 870–899 1.000 57.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG AGAACGAATCACACTTTTACCAC 874–903 1.000 57.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG GAACGAATCACACTTTTACCACT 873–902 1.000 57.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG AGGGTGTAATAGAACGAATCACA 884–913 1.000 57.4
trnG-UCC_p1 trnG-UCC GAATTTTGTGATTCCCGCGG TGCTAAAACAACCCCAAGCT 1715–1743 1.000 83.5
trnG-UCC_p2 trnG-UCC GGAATTTTGTGATTCCCGCG TGCTAAAACAACCCCAAGCT 1716–1744 1.000 83.5
trnG-UCC_p3 trnG-UCC GAATTTTGTGATTCCCGCGG CCGCAGCTCAAATTAAAGCC 1868–1896 1.000 83.1
trnG-UCC_p4 trnG-UCC GGAATTTTGTGATTCCCGCG CCGCAGCTCAAATTAAAGCC 1869–1897 1.000 83.1
trnG-UCC_p5 trnG-UCC GAATTTTGTGATTCCCGCGG TGGCACAATTCGCAGAACTA 1814–1842 1.000 82.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGTTTTCTACTTCAGGA 156–183 1.000 52.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGTTTTCTACTTCAGGAA 156–183 1.000 50.0
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TGGAACGTTTTCTACTTCAGGA 191–218 1.000 49.3
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAAGAACAGATGGAACGTT 167–194 1.000 49.3
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAAGAACAGATGGAACGT 168–195 1.000 49.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC AGATTTTTCCGGGGTCGATG 1142–1171 1.000 85.4
psbM-trnD-GUC_p2 psbM-trnD-GUC AATGAAGAGCGCAGTAGCAA AGATTTTTCCGGGGTCGATG 1140–1169 1.000 85.2
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC CCTTCCCAAGCAGACGATAC 1010–1022 0.833 75.6
psbM-trnD-GUC_p4 psbM-trnD-GUC AATGAAGAGCGCAGTAGCAA CCTTCCCAAGCAGACGATAC 1008–1020 0.833 75.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC TCCTTCCCAAGCAGACGATA 1011–1023 0.833 74.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Cerastium alpinum NC_082439.1 147945 View on NCBI ↗
Cerastium brachypetalum subsp. brachypetalum PP103304.1 148403 View on NCBI ↗
Cerastium fontanum PP103305.1 148669 View on NCBI ↗
Cerastium nigrescens NC_082441.1 147940 View on NCBI ↗
Cerastium pumilum subsp. glutinosum PP103307.1 148897 View on NCBI ↗
Cerastium semidecandrum PP103309.1 148640 View on NCBI ↗