Markers + reference

Moehringia

2 species · Caryophyllaceae · Caryophyllales

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Species 2
Genome length 151–151 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 9 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 648 0.0077 1.00 63.2 yes View details
rps2 LSC 711 0.0000 1.00 26.1 yes View details
rps2-rpoC2 LSC 266 0.0193 0.97 66.1 yes View details
trnT-UGU-trnL-UAA LSC 655 0.0061 1.00 62.3 yes View details
atpE LSC 402 0.0100 1.00 49.1 yes View details
petA-psbJ LSC 897 0.0045 1.00 61.4 yes View details
rpl16 LSC 1301 0.0046 1.00 49.4 yes View details
ycf1 IRb 1878 0.0027 1.00 59.5 no View details
ndhF-rpl32 SSC 620 0.0081 1.00 63.4 yes View details
ndhD SSC 1500 0.0013 1.00 48.3 yes View details
ycf1 SSC 5619 0.0028 1.00 48.3 yes View details
ndhD-psaC SSC 135 0.0296 1.00 63.5 yes View details
psbM-trnD-GUC LSC 560 0.0071 1.00 62.0 yes View details
rpl20-rps12 LSC 792 0.0038 1.00 60.9 yes View details
ndhK LSC 684 0.0029 1.00 60.4 yes View details
psbE-petL LSC 1032 0.0029 1.00 60.4 yes View details
rpoB-trnC-GCA LSC 752 0.0027 1.00 60.3 yes View details
psaA-ycf3 LSC 914 0.0011 0.99 60.3 yes View details
matK LSC 1512 0.0026 1.00 60.2 yes View details
rbcL-accD LSC 767 0.0026 1.00 60.2 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
matK_p1 matK CCACACATTTAGGTAGAATTTCCA TGATAACTCAAGCAACCCCC 1620 1.000 40.2
matK_p2 matK TCCACACATTTAGGTAGAATTTCCA TGATAACTCAAGCAACCCCC 1621 1.000 40.2
matK_p3 matK TCCACACATTTAGGTAGAATTTCC TGATAACTCAAGCAACCCCC 1621 1.000 40.2
matK_p4 matK CCACACATTTAGGTAGAATTTCCA GATAACTCAAGCAACCCCCT 1619 1.000 40.2
matK_p5 matK TCCACACATTTAGGTAGAATTTCCA GATAACTCAAGCAACCCCCT 1620 1.000 40.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGAACACGGAAAGAGAGGGA TAGTAATCAAACCGGGGGAC 822–823 1.000 69.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG TAGTAATCAAACCGGGGGAC 818–819 1.000 68.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TAGTAATCAAACCGGGGGAC 817–818 1.000 68.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGAACACGGAAAGAGAGGGA ATAGTAATCAAACCGGGGGAC 823–824 1.000 65.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CACGGAAAGAGAGGGATTCG ATAGTAATCAAACCGGGGGAC 819–820 1.000 65.1
rps2_p1 rps2 GGAAACCCCCTATTTGCCAA ATAAACCGCAGCATTCCCTT 1444–1453 1.000 79.2
rps2_p2 rps2 TTGGAAACCCCCTATTTGCC ATAAACCGCAGCATTCCCTT 1446–1455 1.000 79.2
rps2_p3 rps2 GGAAACCCCCTATTTGCCAA GGGTTGTGTATCAATGGCCA 1169–1171 1.000 78.9
rps2_p4 rps2 GGAAACCCCCTATTTGCCAA TGGGTTGTGTATCAATGGCC 1170–1172 1.000 78.9
rps2_p5 rps2 TTGGAAACCCCCTATTTGCC GGGTTGTGTATCAATGGCCA 1171–1173 1.000 78.9
rps2-rpoC2_p1 rps2-rpoC2 GGTGACATTCGAGGATTCCA TATTCGGGGGAGAAATGGGA 455–462 1.000 75.0
rps2-rpoC2_p2 rps2-rpoC2 TGACCAAAATGAACTCCCGC TATTCGGGGGAGAAATGGGA 422–429 1.000 74.6
rps2-rpoC2_p3 rps2-rpoC2 GGTGACATTCGAGGATTCCA CGGGGGAGAAATGGGAGATA 451–458 1.000 74.4
rps2-rpoC2_p4 rps2-rpoC2 TGACCAAAATGAACTCCCGC CGGGGGAGAAATGGGAGATA 418–425 1.000 74.1
rps2-rpoC2_p5 rps2-rpoC2 TTCGAGTACCGTGACCAAAA TATTCGGGGGAGAAATGGGA 433–440 1.000 73.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AAAGCTCTTCCGATAAGCCC CCGGATTTGAACTGGGGAAT 921–929 1.000 76.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AAAGCTCTTCCGATAAGCCC AAAGGATTTGCAGTCCTCCG 901–909 1.000 76.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCAGCTCATTTCCCTCTCGT CCGGATTTGAACTGGGGAAT 840–848 1.000 75.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCAGCTCATTTCCCTCTCGT AAAGGATTTGCAGTCCTCCG 820–828 1.000 75.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAGCTCTTCCGATAAGCCCT CCGGATTTGAACTGGGGAAT 920–928 1.000 75.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC TGTCTCCCCTAGTTCCTTGG 701–703 1.000 79.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AATGAAGAGCGCAGTAGCAA TGTCTCCCCTAGTTCCTTGG 699–701 1.000 79.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAAGAGCGCAGTAGC CTCCCCTAGTTCCTTGGGAT 698–700 1.000 78.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AATGAAGAGCGCAGTAGCAA CTCCCCTAGTTCCTTGGGAT 696–698 1.000 78.1
psbM-trnD-GUC_p5 psbM-trnD-GUC ATGAAGAGCGCAGTAGCAAT TGTCTCCCCTAGTTCCTTGG 698–700 1.000 77.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Moehringia bavarica PP165056.1 150826 View on NCBI ↗
Moehringia muscosa PP165057.1 150805 View on NCBI ↗