Markers + reference

Premna

4 species · Lamiaceae · Lamiales

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Species 4
Genome length 153–155 kb
Candidate markers 273
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 304 0.0338 0.92 69.3 yes View details
rps16-trnQ-UUG LSC 1236 0.0174 0.96 67.4 yes View details
atpH-atpI LSC 1025 0.0166 0.97 74.8 yes View details
petN-psbM LSC 997 0.0137 0.97 61.0 yes View details
trnE-UUC-trnT-GGU LSC 565 0.0182 0.99 68.1 yes View details
psaA-ycf3 LSC 776 0.0148 0.94 70.2 yes View details
ndhC-trnV-UAC LSC 1081 0.0165 0.80 58.9 yes View details
ndhF SSC 2265 0.0068 0.98 48.6 yes View details
rpl32-trnL-UAG SSC 448 0.0324 1.00 69.3 yes View details
ccsA SSC 978 0.0034 0.99 46.7 yes View details
ccsA-ndhD SSC 262 0.0370 0.98 63.1 yes View details
ndhD SSC 1503 0.0035 1.00 36.8 yes View details
ndhD-psaC SSC 144 0.0564 0.90 74.4 yes View details
trnF-GAA-ndhJ LSC 682 0.0128 0.95 67.0 yes View details
trnT-UGU-trnL-UAA LSC 729 0.0124 0.97 65.4 yes View details
atpB-rbcl LSC 790 0.0068 0.99 64.8 yes View details
atpA-atpF LSC 92 0.0214 0.74 63.2 yes View details
trnW-CCA-trnP-UGG LSC 172 0.0153 0.95 63.1 yes View details
trnL-UAG-ccsA SSC 97 0.0295 0.81 62.2 yes View details
ndhE-ndhG SSC 232 0.0084 0.93 61.7 yes View details
ycf3-trnS-GGA LSC 852 0.0098 0.97 61.6 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 105 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 370–392 1.000 86.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 384–406 1.000 85.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 383–405 1.000 85.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 385–407 1.000 85.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 422–444 1.000 84.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1323–1367 1.000 84.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1265–1309 1.000 84.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAAATTGAAATGGGGCGTGG 1337–1381 1.000 82.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1279–1323 1.000 82.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAAATTGAAATGGGGCGTGG 1315–1359 1.000 79.3
atpA-atpF_p1 atpA-atpF ACTTGAAGTACGGTACCGGT ATTGGCATGTTGGGAACGAT 210–235 1.000 80.9
atpA-atpF_p2 atpA-atpF TCGCCTACTTGAAGTACGGT ATTGGCATGTTGGGAACGAT 216–241 1.000 80.2
atpA-atpF_p3 atpA-atpF ACTAATTTCGTCGGCTCGAA ATTGGCATGTTGGGAACGAT 136–161 1.000 79.3
atpA-atpF_p4 atpA-atpF ACTTGAAGTACGGTACCGGT TATTGGCATGTTGGGAACGA 211–236 1.000 78.1
atpA-atpF_p5 atpA-atpF TCGCCTACTTGAAGTACGGT TATTGGCATGTTGGGAACGA 217–242 1.000 77.4
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1111–1125 1.000 81.2
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1129–1143 1.000 80.8
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1128–1142 1.000 80.3
atpH-atpI_p4 atpH-atpI AACGGAAGCAGCAGAAATCA TCAGTGGTTCCTATCCCTGT 1172–1186 1.000 80.1
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG TTTTTGCAACTTTAGCCGCG 1123–1137 1.000 79.9
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA AGTTCCTACCGCTTTTCTACT 1071–1086 1.000 63.3
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT AGTTCCTACCGCTTTTCTACT 1069–1084 1.000 63.3
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACCGCT 1078–1093 1.000 63.1
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCT 1076–1091 1.000 63.1
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG AGTTCCTACCGCTTTTCTACT 1068–1083 1.000 62.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 640–715 1.000 84.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 605–680 1.000 84.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 602–677 1.000 84.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 637–712 1.000 83.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 567–642 1.000 83.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Premna microphylla NC_026291.1 155293 View on NCBI ↗
Premna puberula NC_061379.1 153255 View on NCBI ↗
Premna szemaoensis MT473775.1 153396 View on NCBI ↗
Premna vietnamensis MT473774.1 153298 View on NCBI ↗