Markers + reference

Orthosiphon

2 species · Lamiaceae · Lamiales

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Species 2
Genome length 152–152 kb
Candidate markers 268
Primer pairs 80

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 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5553 0.3523 0.88 75.3 yes View details
ndhH SSC 1182 0.4724 0.89 82.0 yes View details
ndhA SSC 2103 0.4682 0.88 80.6 yes View details
ndhI SSC 507 0.4979 0.94 81.5 yes View details
ndhI-ndhG SSC 362 0.5030 0.92 77.9 yes View details
ndhD SSC 1503 0.5000 0.85 80.8 yes View details
ccsA SSC 972 0.4525 0.81 80.0 yes View details
ndhF SSC 2232 0.4555 0.85 79.7 yes View details
trnL-UAG-rpl32 SSC 760 0.4196 0.86 81.0 yes View details
rpl32-ndhF SSC 478 0.3974 0.82 77.3 yes View details
rpl32 SSC 171 0.4500 0.94 76.9 yes View details
ndhE-psaC SSC 254 0.4826 0.91 76.2 yes View details
ccsA-trnL-UAG SSC 116 0.4762 0.91 76.2 yes View details
ndhG SSC 531 0.4244 0.71 75.4 yes View details
ycf1-rps15 SSC 426 0.4241 0.74 74.1 yes View details
ndhE SSC 306 0.4286 0.82 73.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf1_p1 ycf1 TAGCAGAGACCTGGGATAGC CAATGGGGAATTTGCCGAAC 758 0.500 59.9
ycf1_p2 ycf1 ACGGATACTAAGATGCCCGA CAATGGGGAATTTGCCGAAC 1101 0.500 59.9
ycf1_p3 ycf1 TAGCAGAGACCTGGGATAGC AATGGGGAATTTGCCGAACT 757 0.500 59.5
ycf1_p4 ycf1 TAGCAGAGACCTGGGATAGC ATGGGGAATTTGCCGAACTT 756 0.500 59.5
ycf1_p5 ycf1 ACGGATACTAAGATGCCCGA ATGGGGAATTTGCCGAACTT 1099 0.500 59.4
ycf1-rps15_p1 ycf1-rps15 AGCCGAGTTTCACATGACAA CCTGAGTCAGTCTTCCATGC 1000 0.500 57.8
ycf1-rps15_p2 ycf1-rps15 AGCCGAGTTTCACATGACAA AGTCGTTGACGTTTTCCCAA 809 0.500 57.7
ycf1-rps15_p3 ycf1-rps15 AGCCGAGTTTCACATGACAA AACACCATGCATTGATGGGT 1083 0.500 57.5
ycf1-rps15_p4 ycf1-rps15 AGCCGAGTTTCACATGACAA ATATTGCCCAGCTGTTCAGG 1283 0.500 57.5
ycf1-rps15_p5 ycf1-rps15 AGCCGAGTTTCACATGACAA CCAGCTGTTCAGGTCCATTT 1276 0.500 57.3
ndhH_p1 ndhH GCATGGAAGACTGACTCAGG ATGTCTCACCGAATCACACG 1783 0.500 59.8
ndhH_p2 ndhH TTGGGAAAACGTCAACGACT ATGTCTCACCGAATCACACG 1974 0.500 59.8
ndhH_p3 ndhH ATCTCAGAAAGGTTTGCGCA ATGTCTCACCGAATCACACG 1999 0.500 59.1
ndhH_p4 ndhH ACGTCAACGACTACTAGCCT ATGTCTCACCGAATCACACG 1966 0.500 58.5
ndhH_p5 ndhH GCATGGAAGACTGACTCAGG AAGAATTCCCAAAGGACCCG 1430 0.500 58.1
ndhA_p1 ndhA AGAGTCGAAGCACCAAAAGG CGTGGGACAGGGTAATCATG 2479 0.500 58.7
ndhA_p2 ndhA AGTCGAAGCACCAAAAGGAG CGTGGGACAGGGTAATCATG 2477 0.500 58.7
ndhA_p3 ndhA GAGTCGAAGCACCAAAAGGA CGTGGGACAGGGTAATCATG 2478 0.500 58.7
ndhA_p4 ndhA GTCGAAGCACCAAAAGGAGA CGTGGGACAGGGTAATCATG 2476 0.500 58.7
ndhA_p5 ndhA TGATCGGGGATCAGAGTGTT CGTGGGACAGGGTAATCATG 2442 0.500 58.6
ndhI_p1 ndhI ACGGTTCTGTAATAGCGACG CCCAACGGTCCAAAGATGAA 1825 0.500 57.8
ndhI_p2 ndhI GTGACCTATGAGGAGCCGTA CCCAACGGTCCAAAGATGAA 1864 0.500 56.7
ndhI_p3 ndhI ACGGTTCTGTAATAGCGACG AATCCCAATGAAAAGGCCGA 1659 0.500 56.7
ndhI_p4 ndhI ACGGTTCTGTAATAGCGACG ATCCCAATGAAAAGGCCGAA 1658 0.500 56.7
ndhI_p5 ndhI ACGGTTCTGTAATAGCGACG TCCCAATGAAAAGGCCGAAT 1657 0.500 56.7
ndhI-ndhG_p1 ndhI-ndhG CATGATTACCCTGTCCCACG CCCAACGGTCCAAAGATGAA 1080 0.500 58.9
ndhI-ndhG_p2 ndhI-ndhG ACATCAGAACGTTTCCGAGG CCCAACGGTCCAAAGATGAA 1013 0.500 58.6
ndhI-ndhG_p3 ndhI-ndhG TCAAATTGCTTTAGGCCGGT CCCAACGGTCCAAAGATGAA 744 0.500 58.6
ndhI-ndhG_p4 ndhI-ndhG ACAAACAATACGAGCTGCCA CCCAACGGTCCAAAGATGAA 1119 0.500 58.4
ndhI-ndhG_p5 ndhI-ndhG CTTGAACTCCGGTCGACAAA CCCAACGGTCCAAAGATGAA 1134 0.500 58.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Orthosiphon aristatus NC_082580.1 152155 View on NCBI ↗
Orthosiphon aristatus var. aristatus OR790650.1 152170 View on NCBI ↗