Markers + reference

Mentha

10 species · Lamiaceae · Lamiales

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Species 10
Genome length 152–152 kb
Candidate markers 271
Primer pairs 95

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 326 0.0115 0.94 46.7 yes View details
rps16-trnQ-UUG LSC 995 0.0121 0.96 63.6 yes View details
petN-psbM LSC 960 0.0069 1.00 54.6 yes View details
ycf3-trnS-GGA LSC 870 0.0061 0.97 55.9 yes View details
trnT-UGU-trnL-UAA LSC 667 0.0083 0.97 62.1 yes View details
accD LSC 1482 0.0019 1.00 30.8 yes View details
rpl32-trnL-UAG SSC 743 0.0108 1.00 55.6 yes View details
ccsA-ndhD SSC 232 0.0215 1.00 45.2 yes View details
ndhD SSC 1530 0.0027 1.00 35.5 yes View details
ycf1 SSC 5559 0.0055 1.00 41.8 yes View details
rps4-trnT-UGU LSC 439 0.0081 0.95 59.0 yes View details
rpl2-trnH-GUG IRa 119 0.0375 0.95 57.8 no View details
rps2-rpoC2 LSC 222 0.0131 0.98 57.1 yes View details
rpoB-trnC-GCA LSC 1121 0.0038 1.00 56.7 yes View details
atpH-atpI LSC 993 0.0043 0.99 55.9 yes View details
psaA-ycf3 LSC 728 0.0048 1.00 55.5 yes View details
trnG-GCC-trnM-CAU LSC 164 0.0136 0.98 53.4 yes View details
trnE-UUC-trnT-GGU LSC 554 0.0069 1.00 52.4 yes View details
petB LSC 1382 0.0019 0.99 51.3 yes View details
rps3 LSC 663 0.0038 1.00 50.9 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 95 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 372–392 1.000 84.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 386–406 1.000 84.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 385–405 1.000 84.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 387–407 1.000 84.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 424–444 1.000 83.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1093–1152 1.000 84.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1035–1094 1.000 84.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCCAAGAGCACCTCATTTCT GAAATTGAAATGGGGCGTGG 1164–1223 1.000 84.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCTCGCTATTCGGAGGTTC 1048–1107 1.000 84.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCCAAGAGCACCTCATTTCT GAGGTTCGAATCCTTCCGTC 1106–1165 1.000 84.1
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1126–1154 1.000 81.0
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 1144–1172 1.000 80.6
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1143–1171 1.000 80.1
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1138–1166 1.000 79.7
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1078–1106 1.000 79.1
rps2-rpoC2_p1 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TTCGAGGGGGAAATGAGAGA 380–385 1.000 78.1
rps2-rpoC2_p2 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TCGAGGGGGAAATGAGAGAT 379–384 1.000 76.3
rps2-rpoC2_p3 rps2-rpoC2 CATGGCCAAAATGAACTCCC TTCGAGGGGGAAATGAGAGA 401–406 1.000 75.2
rps2-rpoC2_p4 rps2-rpoC2 CCATGGCCAAAATGAACTCC TTCGAGGGGGAAATGAGAGA 402–407 1.000 75.2
rps2-rpoC2_p5 rps2-rpoC2 ATGGCCAAAATGAACTCCCG TTCGAGGGGGAAATGAGAGA 400–405 1.000 74.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG TTTTGGTGATTCAGGCGACA 1151–1357 1.000 84.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA TTTTGGTGATTCAGGCGACA 1150–1356 1.000 84.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG CCGGATTTGAACTGGGGAAA 1130–1336 1.000 84.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA CCGGATTTGAACTGGGGAAA 1129–1335 1.000 84.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAAACCCTGATCGATGAA TTTTGGTGATTCAGGCGACA 1142–1348 1.000 82.8
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACCGCTTTTCTACT 1099–1106 1.000 60.1
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACCGCT 1106–1113 1.000 60.0
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACCGCTT 1106–1113 1.000 58.4
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TTCATTCTAGTTCCTACCGCT 1107–1114 1.000 58.4
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACCGCTTTTCTACTT 1099–1106 1.000 57.9

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
Mentha arvensis PX971240.1 152149 View on NCBI ↗
Mentha canadensis NC_044082.1 152154 View on NCBI ↗
Mentha longifolia NC_032054.1 152041 View on NCBI ↗
Mentha pulegium NC_086489.1 152281 View on NCBI ↗
Mentha spicata NC_037247.1 152132 View on NCBI ↗
Mentha suaveolens NC_086486.1 151824 View on NCBI ↗
Mentha x piperita NC_047475.1 152048 View on NCBI ↗
Mentha x rotundifolia PX971243.1 152045 View on NCBI ↗
Mentha x verticillata NC_063687.1 152026 View on NCBI ↗
Mentha x villosa NC_071750.1 152048 View on NCBI ↗