Markers + reference

Lagochilus

10 species · Lamiaceae · Lamiales

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Species 10
Genome length 151–152 kb
Candidate markers 271
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0017 1.00 38.2 yes View details
rps16-trnQ-UUG LSC 1013 0.0084 1.00 66.6 yes View details
atpH-atpI LSC 961 0.0082 1.00 63.7 yes View details
trnT-CGU-psbD LSC 1254 0.0063 1.00 55.1 yes View details
petA-psbJ LSC 1044 0.0120 1.00 74.5 yes View details
psbE-petL LSC 942 0.0089 1.00 64.7 yes View details
petD LSC 1234 0.0068 1.00 55.5 yes View details
ndhF SSC 2223 0.0047 1.00 61.5 yes View details
ccsA SSC 972 0.0067 1.00 42.1 yes View details
rps15-ycf1 SSC 425 0.0092 1.00 51.7 yes View details
ycf1 SSC 5517 0.0062 1.00 50.1 yes View details
trnK-UUU-rps16 LSC 728 0.0073 0.99 69.4 yes View details
trnH-GUG-psbA LSC 258 0.0223 0.93 68.7 yes View details
trnE-UUC-trnT-CGU LSC 598 0.0052 0.98 67.4 yes View details
rpoB-trnC-GCA LSC 1087 0.0045 1.00 67.2 yes View details
ndhG-ndhI SSC 364 0.0122 1.00 65.2 yes View details
atpB-rbcL LSC 792 0.0062 1.00 63.7 yes View details
petN-psbM LSC 783 0.0081 1.00 62.3 yes View details
ycf4-cemA LSC 560 0.0040 1.00 58.0 yes View details
trnG-GCC-trnfM-CAU LSC 144 0.0148 1.00 57.5 yes View details
rpoB LSC 3219 0.0016 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 105 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 CAACCGTGCTAACCTTGGTA 349–387 1.000 86.9
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 351–389 1.000 86.8
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 363–401 1.000 86.7
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 362–400 1.000 86.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 364–402 1.000 86.6
psbA_p1 psbA GATCCACTTGGCTACATCCG GAAAGCCGTGTGCAATGAAA 1668–1706 1.000 81.3
psbA_p2 psbA CAATCCACTGCCTTGATCCA GAAAGCCGTGTGCAATGAAA 1682–1720 1.000 81.3
psbA_p3 psbA AATCCACTGCCTTGATCCAC GAAAGCCGTGTGCAATGAAA 1681–1719 1.000 81.3
psbA_p4 psbA ACAATCCACTGCCTTGATCC GAAAGCCGTGTGCAATGAAA 1683–1721 1.000 81.3
psbA_p5 psbA GATCCACTTGGCTACATCCG AGTCGGATTTGGCATTTGGA 1908–1948 1.000 80.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGTAAAAGATTCGAGCCGCA TTTCCTTGAAAGGGGTGCTC 873–961 1.000 83.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 849–937 1.000 82.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 848–936 1.000 82.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTTCCTTGAAAGGGGTGCTC 858–946 1.000 81.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGATTCGAGCCGCACTTAAA TTTCCTTGAAAGGGGTGCTC 867–955 1.000 81.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 933–1174 1.000 85.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 875–1116 1.000 85.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 916–1157 1.000 85.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 858–1099 1.000 84.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 934–1175 1.000 84.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCCGTCATGTTCCTTGGATT 1086–1110 1.000 83.0
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA CCCGTCATGTTCCTTGGATT 1102–1126 1.000 82.1
atpH-atpI_p3 atpH-atpI AACGGAAGCGGCAGAAATTA CCCGTCATGTTCCTTGGATT 1084–1108 1.000 81.9
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CCCGTCATGTTCCTTGGATT 1087–1111 1.000 81.9
atpH-atpI_p5 atpH-atpI TAACGGAAGCGGCAGAAATT CCCGTCATGTTCCTTGGATT 1085–1109 1.000 81.9
rpoB_p1 rpoB GTATTCATCTCTGCCGGGTG CTAACAGGGCGAACTGCTAG 228 1.000 79.4
rpoB_p2 rpoB AGTATTCATCTCTGCCGGGT CTAACAGGGCGAACTGCTAG 229 1.000 78.8
rpoB_p3 rpoB TATTCATCTCTGCCGGGTGA CTAACAGGGCGAACTGCTAG 227 1.000 78.8
rpoB_p4 rpoB TCATCTCTGCCGGGTGATAA CTAACAGGGCGAACTGCTAG 224 1.000 78.8
rpoB_p5 rpoB TTCATCTCTGCCGGGTGATA CTAACAGGGCGAACTGCTAG 225 1.000 78.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Lagochilus bungei PQ180373.1 151620 View on NCBI ↗
Lagochilus diacanthophyllus PQ180376.1 151291 View on NCBI ↗
Lagochilus grandiflorus PQ180378.1 151532 View on NCBI ↗
Lagochilus hirtus PQ180379.1 151368 View on NCBI ↗
Lagochilus ilicifolius NC_067785.1 151466 View on NCBI ↗
Lagochilus inebrians PV192925.1 150763 View on NCBI ↗
Lagochilus lanatonodus PQ180381.1 151528 View on NCBI ↗
Lagochilus platyacanthus PQ185532.1 151491 View on NCBI ↗
Lagochilus seravschanicus PQ126530.1 151500 View on NCBI ↗
Lagochilus vvedenskyi PQ126531.1 151159 View on NCBI ↗