Markers + reference

Osmanthus

10 species · Oleaceae · Lamiales

Back to catalogue

Species 10
Genome length 155–155 kb
Candidate markers 265
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS(GCU)-trnG(GCC) LSC 699 0.0054 1.00 50.5 yes View details
psaA-ycf3 LSC 738 0.0051 1.00 46.4 yes View details
atpB-rbcL LSC 792 0.0094 1.00 52.7 yes View details
ycf1 IRb 1164 0.0023 0.99 55.4 no View details
ndhF SSC 2223 0.0035 1.00 42.9 yes View details
ndhF-rpl32 SSC 479 0.0072 1.00 60.9 yes View details
rpl32-trnL(UAG) SSC 542 0.0087 1.00 59.5 yes View details
ycf1 SSC 5607 0.0059 1.00 55.1 yes View details
atpA-atpF LSC 75 0.0265 0.91 65.8 yes View details
matK-rps16 LSC 1640 0.0034 1.00 63.6 yes View details
ndhC-trnM(CAU) LSC 1935 0.0021 1.00 61.9 yes View details
rpl2-trnH(GUG) IRa 76 0.0137 1.00 61.1 no View details
rps2-rpoC2 LSC 205 0.0108 1.00 59.0 yes View details
rps16-trnQ(UUG) LSC 1648 0.0028 1.00 57.5 yes View details
psbE-petL LSC 1182 0.0024 1.00 57.5 yes View details
ycf4-cemA LSC 872 0.0025 1.00 56.1 yes View details
ndhA SSC 2182 0.0012 1.00 55.5 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 CCCTGATCATGAGCAAGTCC GGTGCTCAACCTACAGGAAC 1754–1856 1.000 83.1
matK-rps16_p2 matK-rps16 CCCTGATCATGAGCAAGTCC GTGCTCAACCTACAGGAACT 1753–1855 1.000 77.9
matK-rps16_p3 matK-rps16 CCTGATCATGAGCAAGTCCA GGTGCTCAACCTACAGGAAC 1753–1855 1.000 77.8
matK-rps16_p4 matK-rps16 ACCCTGATCATGAGCAAGTC GGTGCTCAACCTACAGGAAC 1755–1857 1.000 77.7
matK-rps16_p5 matK-rps16 AACCCTGATCATGAGCAAGTC GGTGCTCAACCTACAGGAAC 1756–1858 1.000 75.4
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) CGGATCTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1734–1750 1.000 79.7
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) ATCTGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1731–1747 1.000 79.7
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1720–1736 1.000 79.3
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) CCACAACGGATCTGTCCTTC GAGGTTCGAATCCTTCCGTC 1740–1756 1.000 78.2
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) GGATCTGTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1733–1749 1.000 77.5
trnS(GCU)-trnG(GCC)_p1 trnS(GCU)-trnG(GCC) CAATCCGACGCTTTAGTCCA AGACCGAAAGACCCTTTAACT 798–828 1.000 62.8
trnS(GCU)-trnG(GCC)_p2 trnS(GCU)-trnG(GCC) AATCCGACGCTTTAGTCCAC AGACCGAAAGACCCTTTAACT 797–827 1.000 62.8
trnS(GCU)-trnG(GCC)_p3 trnS(GCU)-trnG(GCC) ATCAACGGAACCGGAAAGAG AGACCGAAAGACCCTTTAACT 862–892 1.000 61.9
trnS(GCU)-trnG(GCC)_p4 trnS(GCU)-trnG(GCC) CATCAACGGAACCGGAAAGA AGACCGAAAGACCCTTTAACT 863–893 1.000 61.1
trnS(GCU)-trnG(GCC)_p5 trnS(GCU)-trnG(GCC) TCATCAACGGAACCGGAAAG AGACCGAAAGACCCTTTAACT 864–894 1.000 61.1
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG TGTTGGGAGCGATGAAAGAA 207–224 1.000 82.5
atpA-atpF_p2 atpA-atpF ATGCCATCGCCTACTTGAAG ATATTGGCATGTTGGGAGCG 216–233 1.000 81.4
atpA-atpF_p3 atpA-atpF ATGCCATCGCCTACTTGAAG ATGTTGGGAGCGATGAAAGA 208–225 1.000 80.7
atpA-atpF_p4 atpA-atpF ATGCCATCGCCTACTTGAAG CATGTTGGGAGCGATGAAAG 209–226 1.000 80.3
atpA-atpF_p5 atpA-atpF CAATGCCATCGCCTACTTGA TGTTGGGAGCGATGAAAGAA 209–226 1.000 80.2
rps2-rpoC2_p1 rps2-rpoC2 AACTCCTGCCTCCATCATCT TTCGAGGGGGAAATGAGAGA 375–379 1.000 79.3
rps2-rpoC2_p2 rps2-rpoC2 TGCCTCCATCATCTCTTCCA TTCGAGGGGGAAATGAGAGA 369–373 1.000 79.2
rps2-rpoC2_p3 rps2-rpoC2 TCCTGCCTCCATCATCTCTT TTCGAGGGGGAAATGAGAGA 372–376 1.000 78.7
rps2-rpoC2_p4 rps2-rpoC2 GAACTCCTGCCTCCATCATC TTCGAGGGGGAAATGAGAGA 376–380 1.000 78.1
rps2-rpoC2_p5 rps2-rpoC2 CTCCTGCCTCCATCATCTCT TTCGAGGGGGAAATGAGAGA 373–377 1.000 77.9
psaA-ycf3_p1 psaA-ycf3 CTTCTGGTTCCGGCGAAC GGAAACAGGCTATAGCGCTT 828–856 1.000 63.4
psaA-ycf3_p2 psaA-ycf3 CTTCTGGTTCCGGCGAAC ATTGGTTGAAGATCACGGGG 780–808 1.000 62.9
psaA-ycf3_p3 psaA-ycf3 CTTCTGGTTCCGGCGAAC TGGTTTGATCAAGCAGCTGA 853–881 1.000 61.4
psaA-ycf3_p4 psaA-ycf3 CTTCTGGTTCCGGCGAAC AGGCTATAGCGCTTACTCCT 822–850 1.000 61.4
psaA-ycf3_p5 psaA-ycf3 CTTCTGGTTCCGGCGAAC TTGGAAACAGGCTATAGCGC 830–858 1.000 61.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Osmanthus aff. armatus Besnard 02-2013 NC_042263.1 155324 View on NCBI ↗
Osmanthus armatus NC_065990.1 155392 View on NCBI ↗
Osmanthus austrocaledonicus MK299397.1 155460 View on NCBI ↗
Osmanthus decorus MK299398.1 155445 View on NCBI ↗
Osmanthus delavayi NC_042462.1 155365 View on NCBI ↗
Osmanthus didymopetalus NC_057502.1 155155 View on NCBI ↗
Osmanthus heterophyllus MK299399.1 155322 View on NCBI ↗
Osmanthus insularis NC_042264.1 155298 View on NCBI ↗
Osmanthus serrulatus MN480301.1 155465 View on NCBI ↗
Osmanthus yunnanensis NC_042463.1 155482 View on NCBI ↗