Markers + reference

Origanum

3 species · Lamiaceae · Lamiales

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Species 3
Genome length 152–152 kb
Candidate markers 274
Primer pairs 115

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 341 0.0156 1.00 68.4 yes View details
rps16 LSC 1145 0.0006 1.00 33.4 yes View details
atpI LSC 744 0.0009 1.00 37.1 yes View details
rpoB-trnC-GCA LSC 1132 0.0018 1.00 46.9 yes View details
trnS-UGA-psbZ LSC 334 0.0020 1.00 40.5 yes View details
clpP1 LSC 1903 0.0014 1.00 58.8 yes View details
ycf1 SSC 1131 0.0006 1.00 59.1 no View details
rpl32-trnL-UAG SSC 722 0.0009 1.00 52.3 yes View details
ccsA SSC 978 0.0007 1.00 35.2 yes View details
ndhD SSC 1389 0.0010 1.00 47.9 yes View details
ndhA SSC 2092 0.0019 1.00 50.1 yes View details
ycf1 SSC 5544 0.0010 1.00 51.2 yes View details
trnL-UAG-ccsA SSC 102 0.0131 1.00 60.8 yes View details
petA-psbJ LSC 996 0.0027 1.00 60.3 yes View details
psaA-pafI LSC 750 0.0000 1.00 60.1 yes View details
rpl16-rps3 LSC 1014 0.0020 1.00 60.0 yes View details
trnT-GGU-psbD LSC 1346 0.0015 1.00 59.9 yes View details
rpl20-rps12 LSC 808 0.0016 1.00 59.8 yes View details
atpH-atpI LSC 1044 0.0016 1.00 59.7 yes View details
petN-psbM LSC 977 0.0007 1.00 59.6 yes View details
pafII-cemA LSC 629 0.0000 1.00 59.6 yes View details
rpoA LSC 1008 0.0013 1.00 59.6 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 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 393–408 1.000 82.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 407–422 1.000 82.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 406–421 1.000 82.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 408–423 1.000 82.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 445–460 1.000 81.6
trnK-UUU_p1 trnK-UUU TGTTCGTGTCAACCAATACCA AGTTTTGTTTAATCGATATTTTCTCG 2688–2689 1.000 40.1
trnK-UUU_p2 trnK-UUU TGTTCGTGTCAACCAATACCA GTTTTGTTTAATCGATATTTTCTCG 2687–2688 1.000 40.1
trnK-UUU_p3 trnK-UUU TGTTCGTGTCAACCAATACCA AAGTTTTGTTTAATCGATATTTTCTCG 2689–2690 1.000 40.1
trnK-UUU_p4 trnK-UUU TGTTCGTGTCAACCAATACCA TTTTGTTTAATCGATATTTTCTCG 2686–2687 1.000 40.1
trnK-UUU_p5 trnK-UUU TGTTCGTGTCAACCAATACCA GTTGAAGTTTTGTTTAATCGATAT 2693–2694 1.000 40.1
rps16_p1 rps16 ATATACAAGCCGCTACCCCC CCCGTTCCAAATTAGAGGAATG 1201 1.000 48.7
rps16_p2 rps16 ATATACAAGCCGCTACCCCC CCCGTTCCAAATTAGAGGAA 1201 1.000 48.3
rps16_p3 rps16 ATATACAAGCCGCTACCCCC CCCGTTCCAAATTAGAGGAAT 1201 1.000 45.0
rps16_p4 rps16 TATACAAGCCGCTACCCCC CCCGTTCCAAATTAGAGGAATG 1200 1.000 44.4
rps16_p5 rps16 TATACAAGCCGCTACCCCC CCCGTTCCAAATTAGAGGAA 1200 1.000 44.0
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1178–1180 1.000 77.2
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 1196–1198 1.000 76.9
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1195–1197 1.000 76.3
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1190–1192 1.000 76.0
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1130–1132 1.000 75.2
atpI_p1 atpI ACATATGCGTTGCTTTGCAC TCCGATTCAAGTAGACAAAGAGA 858–862 1.000 48.2
atpI_p2 atpI CACATATGCGTTGCTTTGCA TCCGATTCAAGTAGACAAAGAGA 859–863 1.000 48.2
atpI_p3 atpI CATATGCGTTGCTTTGCACT TCCGATTCAAGTAGACAAAGAGA 857–861 1.000 46.2
atpI_p4 atpI ATGCGTTGCTTTGCACTAAG TCCGATTCAAGTAGACAAAGAGA 854–858 1.000 45.7
atpI_p5 atpI TCTTGAGCCACATATGCGTT TCCGATTCAAGTAGACAAAGAGA 867–871 1.000 45.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG AACAAGCGGGTTTGATTCCT 1586–1597 1.000 80.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA AACAAGCGGGTTTGATTCCT 1585–1596 1.000 80.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG AGTAAGAGCCCATTCCCCTT 1831–1842 1.000 80.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA AGTAAGAGCCCATTCCCCTT 1830–1841 1.000 80.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG AACAAGCGGGTTTGATTCCT 2186–2197 1.000 80.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Origanum vulgare PQ468695.1 151827 View on NCBI ↗
Origanum vulgare subsp. virens ON641292.1 151826 View on NCBI ↗
Origanum vulgare subsp. vulgare ON641323.1 151830 View on NCBI ↗