Markers + reference

Teucrium

6 species · Lamiaceae · Lamiales

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Species 6
Genome length 150–150 kb
Candidate markers 268
Primer pairs 60

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

2 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
ycf1 SSC 5211 0.0668 0.99 78.9 yes View details
atpF-atpH LSC 354 0.3333 0.00 51.5 yes View details
trnP-UGG-psaJ LSC 283 0.0669 1.00 78.0 yes View details
petA-psbJ LSC 845 0.0124 0.89 69.5 yes View details
rpl16 LSC 1268 0.0260 0.99 69.0 yes View details
rpl32-trnL-UAG SSC 438 0.0384 0.94 67.4 yes View details
rps12-clpP LSC 158 0.0411 0.80 66.6 yes View details
ycf2-trnI-CAU IRa 179 0.0562 0.92 66.3 yes View details
trnI-CAU-ycf2 IRb 179 0.0553 0.92 66.2 yes View details
ycf4-cemA LSC 669 0.0242 0.97 65.8 yes View details
petB LSC 1339 0.0107 1.00 60.3 yes View details
ndhA SSC 2174 0.0136 0.99 59.1 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf4-cemA_p1 ycf4-cemA GTTTATGCTCGTCGTGTCCT TTCGGATTGCCCAGTATTCG 913–954 1.000 87.2
ycf4-cemA_p2 ycf4-cemA AATCGTCGCATATTCCTCCG TTCGGATTGCCCAGTATTCG 982–1023 1.000 86.3
ycf4-cemA_p3 ycf4-cemA CGTCGCATATTCCTCCGATT TTCGGATTGCCCAGTATTCG 979–1020 1.000 86.3
ycf4-cemA_p4 ycf4-cemA AACTTATAGCGGGGTCTCGA TTCGGATTGCCCAGTATTCG 1287–1328 1.000 85.7
ycf4-cemA_p5 ycf4-cemA ACTTATAGCGGGGTCTCGAA TTCGGATTGCCCAGTATTCG 1286–1327 1.000 85.7
petA-psbJ_p1 petA-psbJ GAGAAGGTTCAATTGGCCGA CCGGATTAGGTTCATCCTTGT 901–929 1.000 71.9
petA-psbJ_p2 petA-psbJ TCGAGAAGGTTCAATTGGCC CCGGATTAGGTTCATCCTTGT 903–931 1.000 71.9
petA-psbJ_p3 petA-psbJ AGAAGGTTCAATTGGCCGAA CCGGATTAGGTTCATCCTTGT 900–928 1.000 71.1
petA-psbJ_p4 petA-psbJ CGTGTCCAAGGTCTTTTGGT CCGGATTAGGTTCATCCTTGT 979–1007 1.000 70.6
petA-psbJ_p5 petA-psbJ GAGAAGGTTCAATTGGCCGA GCCGATACTACTGGAAGGAT 998–1026 1.000 69.9
trnP-UGG-psaJ_p1 trnP-UGG-psaJ ACCCGTGACATTTTGTACCC AATAGACCTGCTAAAGCCGC 415–466 1.000 89.6
trnP-UGG-psaJ_p2 trnP-UGG-psaJ CCCGTGACATTTTGTACCCA AATAGACCTGCTAAAGCCGC 414–465 1.000 89.6
trnP-UGG-psaJ_p3 trnP-UGG-psaJ ACAGGATTTGAACCCGTGAC AATAGACCTGCTAAAGCCGC 426–477 1.000 89.5
trnP-UGG-psaJ_p4 trnP-UGG-psaJ CAGGATTTGAACCCGTGACA AATAGACCTGCTAAAGCCGC 425–476 1.000 89.5
trnP-UGG-psaJ_p5 trnP-UGG-psaJ TGACAGGATTTGAACCCGTG AATAGACCTGCTAAAGCCGC 428–479 1.000 89.5
rps12-clpP_p1 rps12-clpP TGACCTTGGTAGTCCGTTCT TACAAAGGACACGCAAACCA 681–717 1.000 86.3
rps12-clpP_p2 rps12-clpP TGACCTTGGTAGTCCGTTCT TAGAAAGCAACGGAGCCATC 1050–1086 1.000 85.7
rps12-clpP_p3 rps12-clpP TGCACCAACGGAAACCATAA TAGAAAGCAACGGAGCCATC 907–941 1.000 85.7
rps12-clpP_p4 rps12-clpP TTGCACCAACGGAAACCATA TAGAAAGCAACGGAGCCATC 908–942 1.000 85.7
rps12-clpP_p5 rps12-clpP TGACCTTGGTAGTCCGTTCT AAGCAACGGAGCCATCATAG 1046–1082 1.000 85.6
petB_p1 petB TTGGTAGTTCGATCGTGGAA TCCTCCCCTTAGTGATAAATGA 1433–1455 1.000 44.7
petB_p2 petB TTTGGTAGTTCGATCGTGGA TCCTCCCCTTAGTGATAAATGA 1434–1456 1.000 44.7
petB_p3 petB TGGTAGTTCGATCGTGGAAT TCCTCCCCTTAGTGATAAATGA 1432–1454 1.000 44.7
petB_p4 petB TTGGTAGTTCGATCGTGGAA TTCCTCCCCTTAGTGATAAATGA 1434–1456 1.000 44.7
petB_p5 petB TTTGGTAGTTCGATCGTGGA TTCCTCCCCTTAGTGATAAATGA 1435–1457 1.000 44.7
rpl16_p1 rpl16 GGATTGCGCCAAAAATTCGA CAAGTACAAATTGCAGGGCG 2004–2021 0.500 65.3
rpl16_p2 rpl16 TGCGCCAAAAATTCGAGTTC CAAGTACAAATTGCAGGGCG 2000–2017 0.500 65.0
rpl16_p3 rpl16 TTGGGTGCCTCAAAATTGGA CAAGTACAAATTGCAGGGCG 2227–2242 0.500 64.2
rpl16_p4 rpl16 GGATTGCGCCAAAAATTCGA GAAATTGCACGTGTCGAGTG 1987–1988 0.333 53.2
rpl16_p5 rpl16 TGCGCCAAAAATTCGAGTTC GAAATTGCACGTGTCGAGTG 1983–1984 0.333 52.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Teucrium chamaedrys PV340612.1 149923 View on NCBI ↗
Teucrium chamaedrys subsp. chamaedrys PP272183.1 149963 View on NCBI ↗
Teucrium mascatense NC_044073.1 150499 View on NCBI ↗
Teucrium montanum PP272184.1 150060 View on NCBI ↗
Teucrium stocksianum subsp. stenophyllum MH325131.1 150087 View on NCBI ↗
Teucrium stocksianum subsp. stocksianum MH325133.1 150076 View on NCBI ↗