Markers + reference

Ocimum

8 species · Lamiaceae · Lamiales

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Species 8
Genome length 152–152 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 301 0.0190 0.99 42.7 yes View details
psbA-matK LSC 556 0.0064 1.00 32.2 yes View details
rps16-trnQ-UUG LSC 913 0.0057 1.00 38.1 yes View details
psbC-trnS-UGA LSC 238 0.0138 0.99 31.2 yes View details
psaA-pafI LSC 803 0.0094 0.99 41.2 yes View details
ycf1 IRb 1131 0.0020 1.00 28.1 no View details
ndhF SSC 2232 0.0061 1.00 28.7 yes View details
psaC-ndhE SSC 260 0.0099 1.00 29.6 yes View details
rps15-ycf1 SSC 442 0.0097 1.00 36.9 yes View details
ycf1 SSC 5535 0.0088 1.00 34.2 yes View details
rpl32-trnL-UAG SSC 726 0.0084 1.00 51.6 yes View details
psbT-pbf1 LSC 65 0.0330 1.00 51.2 yes View details
pafI-trnS-GGA LSC 836 0.0064 1.00 49.1 yes View details
pafII-cemA LSC 648 0.0090 1.00 47.8 yes View details
petA-psbJ LSC 1046 0.0046 1.00 47.7 yes View details
trnE-UUC-trnT-GGU LSC 620 0.0069 1.00 47.4 yes View details
rpoB-trnC-GCA LSC 1227 0.0054 1.00 46.3 yes View details
trnR-UCU-atpA LSC 103 0.0180 1.00 45.3 yes View details
atpF-atpH LSC 305 0.0084 0.94 44.4 yes View details
trnR-ACG-trnN-GUU IRb 571 0.0053 1.00 44.3 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 95 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 363–368 1.000 83.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 377–382 1.000 83.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 376–381 1.000 83.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 378–383 1.000 83.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 415–420 1.000 82.0
psbA-matK_p1 psbA-matK CGGAAACTAAGCTCCCACTC GGATTTTCGGGCGAACCTAT 1695–1711 1.000 81.5
psbA-matK_p2 psbA-matK CGGAAACTAAGCTCCCACTC GAGGAACCCTGCATGCATTA 1667–1683 1.000 81.3
psbA-matK_p3 psbA-matK GGAACCATGCATAGCACTGA GGATTTTCGGGCGAACCTAT 1939–1955 1.000 81.0
psbA-matK_p4 psbA-matK CGGAAACTAAGCTCCCACTC AACCTATGGTTGGTCGAGGA 1698 0.750 69.7
psbA-matK_p5 psbA-matK CGGAAACTAAGCTCCCACTC ACCTATGGTTGGTCGAGGAA 1697 0.750 69.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCCACAACGGGTCATATCCT GAGGTTCGAATCCTTCCGTC 581–1008 1.000 83.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 559–986 1.000 83.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACGGGTCATATCCTT GAGGTTCGAATCCTTCCGTC 580–1007 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAACGGGTCATATCCT TAGCAATTGAAATGGGGCGT 1068 0.750 68.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAGCAATTGAAATGGGGCGT 1046 0.750 67.9
trnR-UCU-atpA_p1 trnR-UCU-atpA AAAAATCGGAATGAACGGCG CGGACCGGTTTCTACTTCAG 224–225 1.000 80.0
trnR-UCU-atpA_p2 trnR-UCU-atpA AAAAATCGGAATGAACGGCG CCGGTTTCTACTTCAGGAGC 220–221 1.000 80.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GAACGGCGTCCATTGTCTAA CCGGTTTCTACTTCAGGAGC 208–209 1.000 80.0
trnR-UCU-atpA_p4 trnR-UCU-atpA GAACGGCGTCCATTGTCTAA CGGACCGGTTTCTACTTCAG 212–213 1.000 79.9
trnR-UCU-atpA_p5 trnR-UCU-atpA ACGGCGTCCATTGTCTAATG CGGACCGGTTTCTACTTCAG 210–211 1.000 79.4
atpF-atpH_p1 atpF-atpH CCAGTAGCCCAAAGAAACGA GGTTGGTTGTAGCACTAGCA 377–394 1.000 81.9
atpF-atpH_p2 atpF-atpH CCAGTAGCCCAAAGAAACGA GGGTTGGTTGTAGCACTAGC 378–395 1.000 79.0
atpF-atpH_p3 atpF-atpH CCAGTAGCCCAAAGAAACGA CCGAGGCAGAGGGAAAAATA 449–466 1.000 76.9
atpF-atpH_p4 atpF-atpH CCAGTAGCCCAAAGAAACGA TGGGTTGGTTGTAGCACTAG 379–396 1.000 76.5
atpF-atpH_p5 atpF-atpH CCAGTAGCCCAAAGAAACGA GCAGAGGGAAAAATACGAGGT 444–461 1.000 74.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG TTTTGGTGATTCAGGCGACA 1367–1415 1.000 83.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA TTTTGGTGATTCAGGCGACA 1366–1414 1.000 83.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTGCCTCGTTTGTATCCCC TTTTGGTGATTCAGGCGACA 1289–1337 1.000 83.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG CCGGATTTGAACTGGGGAAA 1346–1394 1.000 82.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA CCGGATTTGAACTGGGGAAA 1345–1393 1.000 82.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Ocimum americanum NC_079695.1 152460 View on NCBI ↗
Ocimum basilicum NC_035143.1 152407 View on NCBI ↗
Ocimum basilicum var. basilicum OQ706275.1 152407 View on NCBI ↗
Ocimum basilicum var. purpurascens OR478166.1 152407 View on NCBI ↗
Ocimum gratissimum NC_057196.1 152469 View on NCBI ↗
Ocimum kilimandscharicum MW829603.2 151741 View on NCBI ↗
Ocimum tenuiflorum NC_043873.1 151744 View on NCBI ↗
Ocimum x africanum NC_082140.1 152365 View on NCBI ↗