Markers + reference

Dracocephalum

12 species · Lamiaceae · Lamiales

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Species 12
Genome length 149–151 kb
Candidate markers 265
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 373 0.0807 0.91 75.7 yes View details
rps16-trnQ-UUG LSC 912 0.0513 0.99 88.3 yes View details
petN-psbM LSC 947 0.0331 0.98 79.5 yes View details
trnS-UGA-psbZ LSC 334 0.0285 1.00 67.5 yes View details
psaA-ycf3 LSC 798 0.0331 0.96 77.0 yes View details
ycf3-trnS-GGA LSC 504 0.0401 0.90 78.6 yes View details
rps4-trnT-UGU LSC 411 0.0388 0.92 77.8 yes View details
accD LSC 1467 0.0288 1.00 74.0 yes View details
rps11 LSC 228 0.0269 1.00 64.0 yes View details
ndhF SSC 2232 0.0223 1.00 64.5 yes View details
rpl32-trnL-UAG SSC 524 0.0393 0.96 76.6 yes View details
rps15-trnN-GUU SSC 6261 0.0231 1.00 66.5 yes View details
psbI-trnS-GCU LSC 116 0.0396 1.00 80.9 yes View details
psbZ-trnG-GCC LSC 267 0.0479 1.00 77.8 yes View details
trnS-GCU-trnG-UCC LSC 663 0.0311 0.99 77.6 yes View details
trnP-UGG-psaJ LSC 279 0.0299 1.00 76.9 yes View details
ndhC-trnV-UAC LSC 950 0.0272 0.98 76.1 yes View details
trnT-UGU-trnL-UAA LSC 710 0.0242 0.99 75.6 yes View details
trnF-GAA-ndhJ LSC 617 0.0229 1.00 75.2 yes View details
trnE-UUC-trnT-GGU LSC 551 0.0253 0.99 75.0 yes View details
trnG-UCC-trnR-UCU LSC 185 0.0419 1.00 74.9 yes View details
rpl2-trnH-GUG IRa 204 0.0623 0.72 74.7 no 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA AGAAATAGTGGGCGAACGAC TCAGTGCTATGCATGGTTCC 853–885 0.250 56.7
trnH-GUG-psbA_p2 trnH-GUG-psbA AGAAATAGTGGGCGAACGAC CAGTGCTATGCATGGTTCCT 852–884 0.250 56.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AGAAATAGTGGGCGAACGAC CCCTGTTCAGTGCTATGCAT 859–891 0.250 56.7
trnH-GUG-psbA_p4 trnH-GUG-psbA AGAAATAGTGGGCGAACGAC CTGTTGCGTATTCAGCTCCT 1054–1086 0.250 56.1
trnH-GUG-psbA_p5 trnH-GUG-psbA AGAAATAGTGGGCGAACGAC GGTCGTGAATGGGAGCTTAG 1103–1135 0.250 55.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTATCCTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 974–1113 1.000 91.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTATCCTTCAAGTCGCACGT GTCTCGCTATTCGGAGGTTC 987–1126 1.000 91.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 965–1104 1.000 90.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCTCGCTATTCGGAGGTTC 978–1117 1.000 89.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTATCCTTCAAGTCGCACGT CGGGTTTTGGTCTCGCTATT 996–1135 1.000 89.8
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCCGGGCGTA TGGACTAAAGCGTCGGATTG 218–259 1.000 89.5
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCCGGGCGT TGGACTAAAGCGTCGGATTG 219–260 1.000 89.5
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCCGGGCGTA GTGGACTAAAGCGTCGGATT 219–260 1.000 89.5
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCCGGGCGT GTGGACTAAAGCGTCGGATT 220–261 1.000 89.4
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCCGGGCGTA CAATTGGGTGGGAGAGATGG 243–284 1.000 88.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 772–819 1.000 58.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 718–765 0.917 56.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 717–764 0.917 56.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 719–766 0.917 55.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 718–765 0.917 55.2
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 259–279 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 262–282 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU GCTAACGATGTGGGTTCGAT AGAAGACCTCTGTCCTATCCA 249–269 1.000 75.1
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 265–285 1.000 74.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU TTCCAAGCTAACGATGTGGG AGAAGACCTCTGTCCTATCCA 260 0.083 26.1
petN-psbM_p1 petN-psbM GGGGAAGAAGTGGGCTTTAG ACGTAAAAACAGTAAGTCAAAATGA 957–1012 0.833 44.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTAAGTCAAAATGA 1020–1075 0.833 43.8
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA ACGTAAAAACAGTAAGTCAAAATGA 983–1023 0.750 40.6
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT ACGTAAAAACAGTAAGTCAAAATGA 981–1021 0.750 40.6
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG ACGTAAAAACAGTAAGTCAAAATGA 980–1020 0.750 40.6

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
Dracocephalum fragile PV200169.1 150549 View on NCBI ↗
Dracocephalum heterophyllum NC_068133.1 150869 View on NCBI ↗
Dracocephalum komarovii PX928789.1 150880 View on NCBI ↗
Dracocephalum moldavica NC_062584.1 150177 View on NCBI ↗
Dracocephalum nuratavicum PV605700.1 149987 View on NCBI ↗
Dracocephalum officinale NC_066037.1 149817 View on NCBI ↗
Dracocephalum palmatum NC_031874.1 150510 View on NCBI ↗
Dracocephalum rupestre NC_068682.1 151230 View on NCBI ↗
Dracocephalum ruyschiana PQ963003.1 150896 View on NCBI ↗
Dracocephalum seravschanicum PX929666.1 149186 View on NCBI ↗
Dracocephalum taliense NC_058336.1 150976 View on NCBI ↗
Dracocephalum tanguticum NC_057508.1 150954 View on NCBI ↗