Markers + reference

Ballota

2 species · Lamiaceae · Lamiales

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Species 2
Genome length 152–152 kb
Candidate markers 269
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbM-trnD-GUC LSC 547 0.0018 1.00 58.9 yes View details
rps14 LSC 303 0.0000 1.00 24.1 yes View details
rps4 LSC 606 0.0000 1.00 28.3 yes View details
ndhC-trnV-UAC LSC 963 0.0010 1.00 58.5 yes View details
rbcL-accD LSC 690 0.0029 1.00 60.4 yes View details
petD LSC 1208 0.0017 1.00 59.7 yes View details
rps11 LSC 417 0.0000 1.00 33.7 yes View details
rps19 LSC 279 0.0072 1.00 41.8 yes View details
ycf1 IRb 1119 0.0000 1.00 40.0 no View details
rpl32-trnL-UAG SSC 726 0.0028 1.00 60.3 yes View details
ycf1 SSC 5556 0.0005 1.00 52.8 yes View details
rpl36 LSC 114 0.0175 1.00 62.6 yes View details
rps14-psaB LSC 127 0.0157 1.00 61.6 yes View details
rpl22-rps19 LSC 58 0.0172 1.00 60.5 yes View details
trnT-GGU-psbD LSC 1250 0.0016 1.00 59.7 yes View details
trnT-UGU-trnL-UAA LSC 698 0.0014 1.00 59.6 yes View details
trnK-UUU-rps16 LSC 764 0.0013 1.00 59.5 yes View details
rpl20-rps12 LSC 741 0.0014 1.00 59.5 yes View details
rps16-trnQ-UUG LSC 976 0.0010 1.00 59.3 yes View details
rpoB-trnC-GCA LSC 1097 0.0009 1.00 59.3 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 901 1.000 78.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 900 1.000 78.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC TTTCCTTGAAAGGGGTGCTC 915 1.000 77.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTTCCTTGAAAGGGGTGCTC 910 1.000 77.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC TTTCCTTGAAAGGGGTGCTC 887 1.000 76.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 1124 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1107 1.000 78.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1066 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1049 1.000 78.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 1125 1.000 78.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC CCGGATTTGAACTGGGGAAA 1186 1.000 77.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCTGTCAAACCCCGA CCGGATTTGAACTGGGGAAA 1262 1.000 77.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCTGTCAAACCCCG CCGGATTTGAACTGGGGAAA 1263 1.000 77.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC TTTGGGTAATCAGGCGACAC 1206 1.000 76.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCTTCTGTCAAACCCCGA TTTGGGTAATCAGGCGACAC 1282 1.000 76.6
psbM-trnD-GUC_p1 psbM-trnD-GUC TAAGCAGAAAGGCGGTAGGA CCCCTATTTCTTTTCCCCGG 708–709 1.000 76.2
psbM-trnD-GUC_p2 psbM-trnD-GUC TAAGCAGAAAGGCGGTAGGA CCCTATTTCTTTTCCCCGGG 707–708 1.000 76.2
psbM-trnD-GUC_p3 psbM-trnD-GUC ATAAGCAGAAAGGCGGTAGG CCCCTATTTCTTTTCCCCGG 709–710 1.000 74.7
psbM-trnD-GUC_p4 psbM-trnD-GUC ATAAGCAGAAAGGCGGTAGG CCCTATTTCTTTTCCCCGGG 708–709 1.000 74.7
psbM-trnD-GUC_p5 psbM-trnD-GUC TAAGCAGAAAGGCGGTAGGA TCCCCGGGATTGTAGTTCAA 695–696 1.000 74.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1410–1411 1.000 78.7
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1413–1414 1.000 78.5
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1400–1401 1.000 77.6
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1403–1404 1.000 77.5
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1387–1388 1.000 76.9
rps14_p1 rps14 AAGGATTGAATGTGCCCCTC TGGATACTAATAGGACCTGAACCA 448 1.000 45.1
rps14_p2 rps14 GAAGGATTGAATGTGCCCCT TGGATACTAATAGGACCTGAACCA 449 1.000 45.1
rps14_p3 rps14 AAGGATTGAATGTGCCCCTC GGATACTAATAGGACCTGAACCA 447 1.000 43.6
rps14_p4 rps14 AAGGATTGAATGTGCCCCTC TGGATACTAATAGGACCTGAACC 448 1.000 43.6
rps14_p5 rps14 GAAGGATTGAATGTGCCCCT GGATACTAATAGGACCTGAACCA 448 1.000 43.6

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
Ballota nigra NC_066022.1 151909 View on NCBI ↗
Ballota nigra subsp. meridionalis PP840338.1 151930 View on NCBI ↗