Markers + reference

Arenaria

3 species · Caryophyllaceae · Caryophyllales

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Species 3
Genome length 133–146 kb
Candidate markers 271
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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbM-trnD-GUC LSC 500 0.1120 1.00 82.0 yes View details
psbZ-trnG-GCC LSC 301 0.1595 1.00 81.8 yes View details
trnT-UGU-trnL-UAA LSC 604 0.1313 1.00 82.9 yes View details
ndhC-trnV-UAC LSC 551 0.2710 1.00 86.4 yes View details
petA-psbJ LSC 848 0.1223 0.98 82.0 yes View details
trnP-UGG-psaJ LSC 392 0.1190 1.00 69.6 yes View details
ycf1 IRb 1884 0.0297 1.00 68.1 no View details
rpl32-trnL-UAG SSC 788 0.1269 0.70 75.4 yes View details
ndhG-ndhI SSC 378 0.1711 1.00 79.4 yes View details
ycf1 SSC 5601 0.0799 1.00 77.7 yes View details
rpoA LSC 1020 0.0699 1.00 84.9 yes View details
rpl16 LSC 1219 0.0763 1.00 84.8 yes View details
atpB-rbcL LSC 741 0.0787 1.00 84.5 yes View details
rpl20-rps12 LSC 763 0.0764 0.99 84.5 yes View details
matK-trnK-UUU LSC 703 0.0831 1.00 83.7 yes View details
rps16 LSC 1055 0.0756 0.99 83.7 yes View details
accD LSC 1467 0.0688 1.00 83.5 yes View details
atpF-atpH LSC 452 0.0870 1.00 83.4 yes View details
trnE-UUC-trnT-GGU LSC 440 0.1121 1.00 83.4 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
matK-trnK-UUU_p1 matK-trnK-UUU CCGAAGTGTTTGAACCAGGA AACGGTAGAGTACTCGGCTT 1210–1216 0.667 65.6
matK-trnK-UUU_p2 matK-trnK-UUU CCGAAGTGTTTGAACCAGGA ACGGTAGAGTACTCGGCTTT 1209–1215 0.667 65.6
matK-trnK-UUU_p3 matK-trnK-UUU AAGACGGGGCATCTTTCATC AACGGTAGAGTACTCGGCTT 1235–1241 0.667 65.5
matK-trnK-UUU_p4 matK-trnK-UUU AAGACGGGGCATCTTTCATC ACGGTAGAGTACTCGGCTTT 1234–1240 0.667 65.5
matK-trnK-UUU_p5 matK-trnK-UUU CCGAAGTGTTTGAACCAGGA ATGGGGGTTGCTAACTCAAC 1227–1233 0.667 65.2
rps16_p1 rps16 GTTCAGGATCAGTCGTGGTC GAGGTTCGAATCCTTCCGTC 2279–2283 0.667 66.8
rps16_p2 rps16 GTTCAGGATCAGTCGTGGTC AGACCGGTTCCAAATTCGAG 1810–1819 0.667 66.7
rps16_p3 rps16 AGGATCAGTCGTGGTCGTAT GAGGTTCGAATCCTTCCGTC 2275–2279 0.667 66.4
rps16_p4 rps16 AGGATCAGTCGTGGTCGTAT AGACCGGTTCCAAATTCGAG 1806–1815 0.667 66.3
rps16_p5 rps16 GTTCAGGATCAGTCGTGGTC GGTAAGGCATCGGGTTTTGA 2311–2315 0.667 66.1
trnG-UCC_p1 trnG-UCC TATCATGTCCAGTTTCGGCG GAGGAAGCAGAAGCCCTTTT 1241–1246 0.667 65.7
trnG-UCC_p2 trnG-UCC CACGGAAAGAGAGGGATTCG GAGGAAGCAGAAGCCCTTTT 1889–1894 0.667 65.7
trnG-UCC_p3 trnG-UCC GCCCCTTTTCTTGAACCGTA GAGGAAGCAGAAGCCCTTTT 1423–1428 0.667 65.4
trnG-UCC_p4 trnG-UCC TCGGCGTTCGACAAAAGTTA GAGGAAGCAGAAGCCCTTTT 1227–1232 0.667 65.0
trnG-UCC_p5 trnG-UCC ACGGAAAGAGAGGGATTCGA GAGGAAGCAGAAGCCCTTTT 1888–1893 0.667 65.0
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAGAAAACGA TGGTTGTAGCATTAGCCCTT 473–538 1.000 82.1
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGAAAACGA TTGGTTGTAGCATTAGCCCT 474–539 1.000 82.1
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAGAAAACGA TGGTTGTAGCATTAGCCCTTT 473–538 1.000 80.1
atpF-atpH_p4 atpF-atpH CCAGTGACCCAAGAAAACGA TTGGTTGTAGCATTAGCCCTT 474–539 1.000 80.1
atpF-atpH_p5 atpF-atpH CCAGTGACCCAAGAAAACGA TGGTTGTAGCATTAGCCCTTTT 473–538 1.000 73.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC TAGCGGTTCAGGACATCTCT 1051–1191 1.000 90.3
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC TCTAGCGGTTCAGGACATCT 1053–1193 1.000 90.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AATGAAGAGCGCAGTAGCAA TAGCGGTTCAGGACATCTCT 1049–1189 1.000 90.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AATGAAGAGCGCAGTAGCAA TCTAGCGGTTCAGGACATCT 1051–1191 1.000 90.0
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC GTCTAGCGGTTCAGGACATC 1054–1194 1.000 89.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 488–527 1.000 90.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 486–525 1.000 90.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 467–506 1.000 90.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 465–504 1.000 90.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 485–524 1.000 90.3

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
Arenaria leptoclados subsp. leptoclados PP103297.1 146142 View on NCBI ↗
Arenaria roborowskii NC_085474.1 132576 View on NCBI ↗
Arenaria serpyllifolia NC_065316.1 146298 View on NCBI ↗