Markers + reference

Leucas

2 species · Lamiaceae · Lamiales

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Species 2
Genome length 151–152 kb
Candidate markers 267
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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 952 0.0133 0.95 60.2 yes View details
trnS-GCU-trnS-CGA LSC 687 0.0196 0.96 67.6 yes View details
atpH-atpI LSC 989 0.0198 0.97 58.8 yes View details
trnF-GAA-ndhJ LSC 663 0.0201 0.98 63.2 yes View details
ndhC-trnI-AAU LSC 966 0.0187 1.00 58.1 yes View details
atpB-rbcL LSC 795 0.0164 1.00 55.0 yes View details
petA-psbJ LSC 990 0.0173 0.99 60.8 yes View details
ndhF SSC 2223 0.0130 1.00 50.3 yes View details
rpl32-trnL-UAG SSC 715 0.0241 0.99 66.0 yes View details
ycf1 SSC 5538 0.0164 1.00 47.1 yes View details
ndhH-rps15 SSC 100 0.0400 1.00 74.1 yes View details
trnM-CAU-rps14 LSC 149 0.0403 1.00 69.2 yes View details
trnT-UGU-trnL-UAA LSC 654 0.0138 1.00 66.7 yes View details
ndhI-ndhA SSC 86 0.0233 1.00 65.9 yes View details
atpF LSC 1218 0.0100 0.99 65.5 yes View details
ndhK LSC 678 0.0089 1.00 63.8 yes View details
rpl20-rps12 LSC 738 0.0135 1.00 63.4 yes View details
psbE-petL LSC 927 0.0065 1.00 62.5 yes View details
trnL-UAG-ccsA SSC 85 0.0353 1.00 61.6 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 990–1042 1.000 83.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 973–1025 1.000 83.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 991–1043 1.000 82.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 988–1040 1.000 81.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 987–1039 1.000 81.4
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA ACCACTAAACTATACCCGCT 727–742 1.000 65.3
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC ACCACTAAACTATACCCGCT 726–741 1.000 65.3
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA ACCACTAAACTATACCCGCT 781–796 1.000 63.8
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC ACCACTAAACTATACCCGCT 729–744 1.000 62.4
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CGACGCTTTAGTCCACTCAG ACCACTAAACTATACCCGCT 722–737 1.000 62.3
trnS-CGA_p1 trnS-CGA CAATCCGACGCTTTAGTCCA AAGGACTCAAGTGTCTCGGA 1772–1786 1.000 82.5
trnS-CGA_p2 trnS-CGA AATCCGACGCTTTAGTCCAC AAGGACTCAAGTGTCTCGGA 1771–1785 1.000 82.5
trnS-CGA_p3 trnS-CGA CAATCCGACGCTTTAGTCCA CCCTCTTGCGGTAGAAGAAC 2042–2056 1.000 82.2
trnS-CGA_p4 trnS-CGA AATCCGACGCTTTAGTCCAC CCCTCTTGCGGTAGAAGAAC 2041–2055 1.000 82.2
trnS-CGA_p5 trnS-CGA GGATCTCAGTGCAACGTTCT AAGGACTCAAGTGTCTCGGA 1175 0.500 59.3
atpF_p1 atpF TGCCTTAGGGTAGATAATACT AAAAAGAGGGGCAAAGTGGT 1343–1350 1.000 41.5
atpF_p2 atpF TGCCTTAGGGTAGATAATACT AAGAGGGGCAAAGTGGTAGA 1340–1347 1.000 41.5
atpF_p3 atpF TGCCTTAGGGTAGATAATACT AGAGGGGCAAAGTGGTAGAA 1339–1346 1.000 41.5
atpF_p4 atpF ATGCCTTAGGGTAGATAATACT AAAAAGAGGGGCAAAGTGGT 1344–1351 1.000 41.5
atpF_p5 atpF ATGCCTTAGGGTAGATAATACT AGAGGGGCAAAGTGGTAGAA 1340–1347 1.000 41.5
atpH-atpI_p1 atpH-atpI CTTGGACTACGAACGGGAAG TGCTTTGGCTTTACTCACGT 1729–1758 1.000 82.2
atpH-atpI_p2 atpH-atpI CTCATCTGCGAATCAGCCTT TGCTTTGGCTTTACTCACGT 1682–1711 1.000 81.9
atpH-atpI_p3 atpH-atpI CTTGGACTACGAACGGGAAG GCCGCACCTACGAATGATAT 1761–1790 1.000 81.8
atpH-atpI_p4 atpH-atpI CTTGGACTACGAACGGGAAG GGCAAATAGGGGGTTTCCAA 2060–2089 1.000 81.7
atpH-atpI_p5 atpH-atpI CTTGGACTACGAACGGGAAG TTGGCAAATAGGGGGTTTCC 2062–2091 1.000 81.7
trnM-CAU-rps14_p1 trnM-CAU-rps14 GCTACCAAACTGCTCTACCC CGTTGTTTTTCGACCGGAAG 293 1.000 81.3
trnM-CAU-rps14_p2 trnM-CAU-rps14 AAGGTTATGAGCCTTGCGAG CGTTGTTTTTCGACCGGAAG 312 1.000 81.2
trnM-CAU-rps14_p3 trnM-CAU-rps14 GCTACCAAACTGCTCTACCC CGCGAGCTAACTATCGAGAC 271 1.000 81.1
trnM-CAU-rps14_p4 trnM-CAU-rps14 GATGTTGCGGAGACAGGATT CGTTGTTTTTCGACCGGAAG 347 1.000 81.0
trnM-CAU-rps14_p5 trnM-CAU-rps14 TTTGAACCCGTGACCTCAAG CGTTGTTTTTCGACCGGAAG 329 1.000 81.0

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
Leucas ciliata PV802396.1 151259 View on NCBI ↗
Leucas mollissima OR565912.1 151603 View on NCBI ↗