Markers + reference

Rotheca

2 species · Lamiaceae · Lamiales

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Species 2
Genome length 150–151 kb
Candidate markers 272
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 6 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5577 0.3637 0.88 75.9 yes View details
ycf1-rps15 SSC 406 0.4850 0.82 76.0 yes View details
ndhH SSC 1182 0.4947 0.64 74.8 yes View details
ndhA SSC 2086 0.4769 0.81 78.5 yes View details
ndhI SSC 507 0.4896 0.95 81.6 yes View details
ndhI-ndhG SSC 352 0.5171 0.91 77.4 yes View details
ndhG SSC 531 0.5111 0.85 79.3 yes View details
ndhE-psaC SSC 250 0.4622 0.90 75.9 yes View details
psaC SSC 246 0.5588 0.83 74.0 yes View details
ccsA SSC 972 0.4849 0.85 80.9 yes View details
ycf1 IRa 1079 0.0019 1.00 44.9 no View details
ndhD SSC 1503 0.4725 0.92 82.8 yes View details
ndhF SSC 2217 0.4498 0.81 78.3 yes View details
rpl32-ndhF SSC 510 0.4504 0.81 77.9 yes View details
trnL-UAG-rpl32 SSC 339 0.4598 0.92 77.2 yes View details
ndhE SSC 306 0.4747 0.97 75.5 yes View details
rps15-ndhH SSC 104 0.5165 0.88 75.3 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf1_p1 ycf1 CATTTATCTCCGACCGGGTG GCGGGAGTTTGGTGGATTTA 588 0.500 57.6
ycf1_p2 ycf1 CATTTATCTCCGACCGGGTG AGATCCTTTGCGGGAGTTTG 597 0.500 57.5
ycf1_p3 ycf1 CATTTATCTCCGACCGGGTG GATCTTCCCACCACCTTGTG 868 0.500 57.5
ycf1_p4 ycf1 CATTTATCTCCGACCGGGTG CCAGACAGACGAATGGGTTC 1223 0.500 56.7
ycf1_p5 ycf1 TCCACCCCTTTCTTAAGCCT GCGGGAGTTTGGTGGATTTA 725 0.500 56.7
ycf1-rps15_p1 ycf1-rps15 CGGAAAGAACAGTAGCCAGG CAGCAGTCGTTGACGTTTTC 782 0.500 57.8
ycf1-rps15_p2 ycf1-rps15 GAACCCATTCGTCTGTCTGG CAGCAGTCGTTGACGTTTTC 1093 0.500 57.8
ycf1-rps15_p3 ycf1-rps15 CGGAAAGAACAGTAGCCAGG TCAAATGGTATCGCGCTTCA 893 0.500 57.7
ycf1-rps15_p4 ycf1-rps15 GAACCCATTCGTCTGTCTGG TCAAATGGTATCGCGCTTCA 1204 0.500 57.7
ycf1-rps15_p5 ycf1-rps15 CGGAAAGAACAGTAGCCAGG AGTCGTTGACGTTTTCCCAA 778 0.500 57.6
rps15-ndhH_p1 rps15-ndhH GAAAACGTCAACGACTGCTG TCCGGAAGCTCGTAACATTG 889 0.500 59.9
rps15-ndhH_p2 rps15-ndhH TTGGGAAAACGTCAACGACT TCCGGAAGCTCGTAACATTG 893 0.500 59.7
rps15-ndhH_p3 rps15-ndhH GAAAACGTCAACGACTGCTG CGTAACATTGGCCCCGATAA 879 0.500 59.6
rps15-ndhH_p4 rps15-ndhH TTGGGAAAACGTCAACGACT CGTAACATTGGCCCCGATAA 883 0.500 59.4
rps15-ndhH_p5 rps15-ndhH GAAAACGTCAACGACTGCTG ATCAGTCGAAGAACACCGTG 291 0.500 59.4
ndhH_p1 ndhH GAAAACGTCAACGACTGCTG CGTTGTTGTATCCCTGCAGA 1570 0.500 59.2
ndhH_p2 ndhH TGAAGCGCGATACCATTTGA CGTTGTTGTATCCCTGCAGA 1459 0.500 59.1
ndhH_p3 ndhH GAAAACGTCAACGACTGCTG AGCAGCCCTTAATCCACCTA 1883 0.500 59.1
ndhH_p4 ndhH TTGGGAAAACGTCAACGACT CGTTGTTGTATCCCTGCAGA 1574 0.500 59.0
ndhH_p5 ndhH TGCATGGAAGAATGACTCGG CGTTGTTGTATCCCTGCAGA 1394 0.500 59.0
ndhA_p1 ndhA GCCCGGTTTTATCAACTTGC AGCCACGATTGATTCTCACC 2905 0.500 59.7
ndhA_p2 ndhA GCCCGGTTTTATCAACTTGC TCCATTATTGATGCCGGCAA 2734 0.500 59.4
ndhA_p3 ndhA GCCCGGTTTTATCAACTTGC TTCCATTATTGATGCCGGCA 2735 0.500 59.4
ndhA_p4 ndhA CAATGTTACGAGCTTCCGGA TGGCAGCTCGTATTGTTTGT 2743 0.500 59.1
ndhA_p5 ndhA CAGGCTCTGGAAGGAATTCC TCCATTATTGATGCCGGCAA 2973 0.500 59.1
ndhI_p1 ndhI CTCTAGCCGAGTGTGAGAGA AGCCACGATTGATTCTCACC 1131 0.500 59.5
ndhI_p2 ndhI TCTCTAGCCGAGTGTGAGAG AGCCACGATTGATTCTCACC 1132 0.500 59.5
ndhI_p3 ndhI CTCTAGCCGAGTGTGAGAGA AAGACCCGATCCCAGAAAGA 1424 0.500 59.4
ndhI_p4 ndhI TCTCTAGCCGAGTGTGAGAG AAGACCCGATCCCAGAAAGA 1425 0.500 59.4
ndhI_p5 ndhI CTCTAGCCGAGTGTGAGAGA ATGATCCCATACCAGGACGT 1738 0.500 58.9

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
Rotheca myricoides NC_059906.1 150596 View on NCBI ↗
Rotheca serrata MT473776.1 150371 View on NCBI ↗