Markers + reference

Thymus

12 species · Lamiaceae · Lamiales

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Species 12
Genome length 152–152 kb
Candidate markers 271
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 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
trnH-GUG-psbA LSC 322 0.0290 1.00 76.4 yes View details
rps16-trnQ-UUG LSC 915 0.0088 1.00 53.7 yes View details
rpoC1 LSC 2805 0.0213 1.00 65.6 yes View details
trnT-UGU-trnL-UAA LSC 676 0.0088 1.00 55.7 yes View details
ycf1 SSC 5544 0.0078 1.00 53.0 yes View details
rpoC2-rpoC1 LSC 149 0.0521 1.00 69.0 yes View details
infA-rps8 LSC 127 0.0214 0.98 67.1 yes View details
trnE-UUC-trnT-GGU LSC 564 0.0063 1.00 60.6 yes View details
rpl32-trnL-UAG SSC 726 0.0067 1.00 60.3 yes View details
petN-psbM LSC 976 0.0054 1.00 59.8 yes View details
trnK-UUU-rps16 LSC 546 0.0058 1.00 59.5 yes View details
petA-psbJ LSC 994 0.0038 1.00 58.8 yes View details
psaA-ycf3 LSC 765 0.0055 1.00 58.1 yes View details
ndhC-trnV-UAC LSC 968 0.0053 1.00 57.9 yes View details
rpoB-trnC-GCA LSC 1129 0.0058 1.00 57.6 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 75 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 TTCCCTCTAGACCTAGCTGC 374–394 1.000 88.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 388–408 1.000 87.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 387–407 1.000 87.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 389–409 1.000 87.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 426–446 1.000 86.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC CCTTGAAAAAGGCGCTCAAC 681–700 1.000 81.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC CTTGAAAAAGGCGCTCAACC 680–699 1.000 81.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CCTTGAAAAAGGCGCTCAAC 676–695 1.000 81.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CTTGAAAAAGGCGCTCAACC 675–694 1.000 81.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC TCCTTGAAAAAGGCGCTCAA 682–701 1.000 81.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 983–1035 1.000 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCTCGCTATTCGGAGGTTC 996–1048 1.000 83.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAAAATCCACAACGGGTCGT GAGGTTCGAATCCTTCCGTC 1010–1062 1.000 82.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGGGTTTTGGTCTCGCTATT 1005–1057 1.000 82.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAAAATCCACAACGGGTCGT GTCTCGCTATTCGGAGGTTC 1023–1075 1.000 81.8
rpoC2-rpoC1_p1 rpoC2-rpoC1 GCCATTCCGAAGTGCTCTAT GGCCTGTTCATATGGTATCT 281–292 0.917 47.7
rpoC2-rpoC1_p2 rpoC2-rpoC1 TGAAAGACCAGATTGGCTCG GGCCTGTTCATATGGTATCT 212 0.833 44.6
rpoC2-rpoC1_p3 rpoC2-rpoC1 AAGACCAGATTGGCTCGTTC GGCCTGTTCATATGGTATCT 209 0.833 44.6
rpoC2-rpoC1_p4 rpoC2-rpoC1 GAAAGACCAGATTGGCTCGT GGCCTGTTCATATGGTATCT 211 0.833 44.6
rpoC2-rpoC1_p5 rpoC2-rpoC1 TATGCCATTCCGAAGTGCTC GGCCTGTTCATATGGTATCT 284 0.833 44.5
rpoC1_p1 rpoC1 AGTAAAGAGGTCTGCATTCCT AGGAAGGAAGCTTAATCGGA 2890–2908 0.917 40.0
rpoC1_p2 rpoC1 AGTTGAAGTAAAGAGGTCTGCA AGGAAGGAAGCTTAATCGGA 2896–2914 0.917 39.7
rpoC1_p3 rpoC1 GAGGTCTGCATTCCTATATCGT AGGAAGGAAGCTTAATCGGA 2884–2902 0.917 38.9
rpoC1_p4 rpoC1 AGTAAAGAGGTCTGCATTCCT ACGATCTTTAGCTCTGGAACTG 2951–2963 0.833 35.7
rpoC1_p5 rpoC1 AGTTGAAGTAAAGAGGTCTGCA ACGATCTTTAGCTCTGGAACTG 2957–2969 0.833 35.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG TTTTGGTGATTCAGGCGACA 1304–1327 1.000 82.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA TTTTGGTGATTCAGGCGACA 1303–1326 1.000 82.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG CCGGATTTGAACTGGGGAAA 1283–1306 1.000 82.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA CCGGATTTGAACTGGGGAAA 1282–1305 1.000 82.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAAACCCTGATCGATGAA TTTTGGTGATTCAGGCGACA 1295–1318 1.000 81.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Thymus japonicus NC_046822.1 151782 View on NCBI ↗
Thymus linearis NC_071852.1 151828 View on NCBI ↗
Thymus mastichina NC_086485.1 151722 View on NCBI ↗
Thymus mongolicus NC_046520.1 151834 View on NCBI ↗
Thymus praecox subsp. polytrichus PP272181.1 151747 View on NCBI ↗
Thymus praecox subsp. praecox PP272182.1 151763 View on NCBI ↗
Thymus quinquecostatus NC_069224.1 151802 View on NCBI ↗
Thymus seravschanicus PQ115142.1 151712 View on NCBI ↗
Thymus serpyllum NC_081477.1 152048 View on NCBI ↗
Thymus subnervosus PZ130073.1 151784 View on NCBI ↗
Thymus villosus subsp. lusitanicus ON641262.1 151830 View on NCBI ↗
Thymus vulgaris NC_086487.1 151649 View on NCBI ↗