Markers + reference

Lycopus

3 species · Lamiaceae · Lamiales

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Species 3
Genome length 152–152 kb
Candidate markers 268
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 555 0.0078 1.00 62.9 yes View details
trnT-GGU-psbD LSC 1386 0.0038 1.00 48.7 yes View details
ycf3 LSC 1946 0.0031 1.00 57.2 yes View details
rpl16 LSC 1281 0.0016 1.00 48.1 yes View details
rpl32-trnL-UAG SSC 757 0.0066 1.00 55.9 yes View details
ndhD SSC 1530 0.0009 1.00 33.8 yes View details
ndhE SSC 306 0.0065 1.00 32.6 yes View details
ndhG-ndhI SSC 374 0.0071 1.00 42.1 yes View details
rps15-ycf1 SSC 442 0.0045 1.00 34.8 yes View details
ycf1 SSC 5553 0.0028 1.00 54.3 yes View details
trnR-UCU-atpA LSC 108 0.0123 1.00 61.4 yes View details
ycf3-trnS-GGA LSC 632 0.0011 1.00 61.2 yes View details
rpoB-trnC-GCA LSC 1182 0.0011 0.99 59.9 yes View details
ndhC-trnM-CAU LSC 1787 0.0019 1.00 59.5 yes View details
petA-psbJ LSC 1036 0.0006 1.00 59.4 yes View details
psbC LSC 1422 0.0009 1.00 59.3 yes View details
rps2-rpoC2 LSC 214 0.0093 1.00 58.5 yes View details
rps8-rpl14 LSC 190 0.0035 0.99 57.6 yes View details
rps19 LSC 279 0.0072 1.00 57.1 yes View details
rpoC1 LSC 2800 0.0010 1.00 57.0 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTCAAAAGTT CTTTTAAAGAAGGCGGGGGT 731–732 1.000 79.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCGGTCTTCAAAAGTT TCTTTTAAAGAAGGCGGGGG 732–733 1.000 78.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC CTTTTAAAGAAGGCGGGGGT 662–663 1.000 78.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CTTTTAAAGAAGGCGGGGGT 657–658 1.000 77.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCGGTCTTCAAAAGTT AGGCGGGGGTTTTTAAAGAA 721–722 1.000 77.3
trnR-UCU-atpA_p1 trnR-UCU-atpA AAAAATCGGAATGAACGGCG CCGGTTTCTACTTCAGGAGC 224–226 1.000 78.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GAACGGCGTCCATTGTCTAA CCGGTTTCTACTTCAGGAGC 212–214 1.000 78.8
trnR-UCU-atpA_p3 trnR-UCU-atpA ACGGCGTCCATTGTCTAATG CCGGTTTCTACTTCAGGAGC 210–212 1.000 78.3
trnR-UCU-atpA_p4 trnR-UCU-atpA AAAAATCGGAATGAACGGCG TTCAGGAACAAATGGACCGG 240–242 1.000 78.2
trnR-UCU-atpA_p5 trnR-UCU-atpA GAACGGCGTCCATTGTCTAA TTCAGGAACAAATGGACCGG 228–230 1.000 78.0
rps2-rpoC2_p1 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TTCGAGGGGGAAATGAGAGA 377–379 1.000 76.0
rps2-rpoC2_p2 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TCGAGGGGGAAATGAGAGAT 376–378 1.000 74.2
rps2-rpoC2_p3 rps2-rpoC2 CATGGCCAAAATGAACTCCC TTCGAGGGGGAAATGAGAGA 398–400 1.000 73.2
rps2-rpoC2_p4 rps2-rpoC2 CCATGGCCAAAATGAACTCC TTCGAGGGGGAAATGAGAGA 399–401 1.000 73.2
rps2-rpoC2_p5 rps2-rpoC2 ATGGCCAAAATGAACTCCCG TTCGAGGGGGAAATGAGAGA 397–399 1.000 72.1
rpoC1_p1 rpoC1 AGTGAAGAGGTCTGCATTCC CTGCTTGTTCGAGAACTACGA 2963–2972 1.000 65.6
rpoC1_p2 rpoC1 GTGAAGAGGTCTGCATTCCT CTGCTTGTTCGAGAACTACGA 2962–2971 1.000 65.6
rpoC1_p3 rpoC1 AGTGAAGAGGTCTGCATTCC TGCTTGTTCGAGAACTACGA 2962–2971 1.000 65.6
rpoC1_p4 rpoC1 GTGAAGAGGTCTGCATTCCT TGCTTGTTCGAGAACTACGA 2961–2970 1.000 65.6
rpoC1_p5 rpoC1 GTGAAGAGGTCTGCATTCCT ACTGCTTGTTCGAGAACTACG 2963–2972 1.000 63.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG TTTTGGTGATTCAGGCGACA 1363–1369 1.000 80.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA TTTTGGTGATTCAGGCGACA 1362–1368 1.000 80.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG CCGGATTTGAACTGGGGAAA 1342–1348 1.000 79.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA CCGGATTTGAACTGGGGAAA 1341–1347 1.000 79.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAAACCCTGATCGATGAA TTTTGGTGATTCAGGCGACA 1354–1360 1.000 78.3
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1546–1566 1.000 79.0
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1549–1569 1.000 78.8
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1536–1556 1.000 77.9
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1539–1559 1.000 77.8
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1523–1543 1.000 77.2

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
Lycopus europaeus NC_064128.1 152085 View on NCBI ↗
Lycopus lucidus PV558881.1 152112 View on NCBI ↗
Lycopus lucidus var. hirtus MT980792.1 152096 View on NCBI ↗