Markers + reference

Ajuga

15 species · Lamiaceae · Lamiales

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Species 15
Genome length 150–151 kb
Candidate markers 272
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

15 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 821 0.0142 1.00 68.1 yes View details
trnS-GCU-trnG-UCC LSC 700 0.0109 0.97 66.2 yes View details
atpF-atpH LSC 357 0.0198 1.00 53.9 yes View details
rps2-rpoC2 LSC 235 0.0216 0.99 61.5 yes View details
trnT-UGU-trnL-UAA LSC 636 0.0131 1.00 60.5 yes View details
ndhC-trnV-UAC LSC 834 0.0142 0.99 65.3 yes View details
petA-psbJ LSC 893 0.0102 1.00 63.2 yes View details
rpl16 LSC 1237 0.0077 1.00 53.5 yes View details
ycf1 IRb 1155 0.0015 1.00 40.6 no View details
ndhF SSC 2241 0.0076 1.00 59.5 yes View details
ndhF-rpl32 SSC 536 0.0155 1.00 62.5 yes View details
ccsA SSC 972 0.0056 1.00 50.5 yes View details
ndhE SSC 306 0.0026 1.00 22.8 yes View details
ndhE-ndhG SSC 233 0.0241 1.00 63.8 yes View details
ycf1 SSC 5427 0.0086 1.00 49.8 yes View details
trnK-UUU-rps16 LSC 893 0.0107 1.00 70.3 yes View details
psbI-trnS-GCU LSC 115 0.0349 1.00 69.1 yes View details
trnL-UAG-ccsA SSC 93 0.0225 1.00 67.5 yes View details
trnH-GUG-psbA LSC 331 0.0119 0.98 67.4 yes View details
atpH-atpI LSC 968 0.0094 1.00 66.8 yes View details
ccsA-ndhD SSC 254 0.0254 0.96 66.2 yes View details
pafII-cemA LSC 652 0.0072 1.00 63.7 yes View details
atpA-atpF LSC 114 0.0198 1.00 63.5 yes View details
petN-psbM LSC 539 0.0057 1.00 62.1 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 115 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 292–398 1.000 86.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 306–412 1.000 86.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 305–411 1.000 86.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 307–413 1.000 86.1
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 321–427 1.000 83.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CCACAGGAACCGTTCAGAAT 977–1014 1.000 84.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCACAGGAACCGTTCAGAAT 976–1013 1.000 84.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC CCACAGGAACCGTTCAGAAT 991–1028 1.000 84.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CCACAGGAACCGTTCAGAAT 986–1023 1.000 84.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC CCACAGGAACCGTTCAGAAT 963–1000 1.000 82.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TCGGAGGTTCGAATCCTTTC 521–1310 1.000 83.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TAAGGCAACGGGTTTTGGTC 548–1337 1.000 82.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGGAGGTTCGAATCCTTTC 504–1293 1.000 82.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 531–1320 1.000 82.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGCATCCCCATTCCTAGACA TCGGAGGTTCGAATCCTTTC 570–1359 1.000 82.2
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 223–244 1.000 86.4
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 224–245 1.000 86.4
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 224–245 1.000 86.4
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 225–246 1.000 86.3
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA ATCTTGGGAGAGATGGCTGA 244–265 1.000 84.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CGCAAGGCCCTTTAACTTTA 638–802 1.000 73.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CGCAAGGCCCTTTAACTTTA 637–801 1.000 73.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CGCAAGGCCCTTTAACTTTA 692–856 1.000 72.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CGCAAGGCCCTTTAACTTTAA 638–802 1.000 71.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CGCAAGGCCCTTTAACTTTAA 637–801 1.000 71.9
atpA-atpF_p1 atpA-atpF TTTCGTCAGCTCGAATGGTT ACAAGGAGCTCTAGGGACTC 211–249 1.000 84.8
atpA-atpF_p2 atpA-atpF CCGTCGCCTACTTGAAGTAC ACAAGGAGCTCTAGGGACTC 299–337 1.000 84.7
atpA-atpF_p3 atpA-atpF GTCGCCTACTTGAAGTACGG ACAAGGAGCTCTAGGGACTC 297–335 1.000 84.7
atpA-atpF_p4 atpA-atpF CCGTCGCCTACTTGAAGTAC TTGGGGGCGATGAAAGAAAT 220–258 0.933 81.7
atpA-atpF_p5 atpA-atpF GTCGCCTACTTGAAGTACGG TTGGGGGCGATGAAAGAAAT 218–256 0.933 81.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Ajuga bracteosa NC_068635.1 150343 View on NCBI ↗
Ajuga campylantha NC_084165.1 150453 View on NCBI ↗
Ajuga decumbens MF967578.1 150377 View on NCBI ↗
Ajuga forrestii NC_048512.1 150492 View on NCBI ↗
Ajuga genevensis PP024532.1 149753 View on NCBI ↗
Ajuga lupulina PV243805.1 150368 View on NCBI ↗
Ajuga macrosperma NC_084166.1 150362 View on NCBI ↗
Ajuga multiflora PQ178989.1 149745 View on NCBI ↗
Ajuga nipponensis NC_084167.1 150442 View on NCBI ↗
Ajuga nubigena NC_071844.1 150490 View on NCBI ↗
Ajuga ovalifolia NC_084168.1 150443 View on NCBI ↗
Ajuga pyramidalis subsp. pyramidalis PP024533.1 150099 View on NCBI ↗
Ajuga reptans NC_023102.1 149963 View on NCBI ↗
Ajuga spectabilis NC_065098.1 150417 View on NCBI ↗
Ajuga turkestanica PV192927.1 150719 View on NCBI ↗