Markers + reference

Lomatogonium

2 species · Gentianaceae · Gentianales

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Species 2
Genome length 152–152 kb
Candidate markers 255
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 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5478 0.3584 0.88 75.2 yes View details
ndhH SSC 1182 0.4782 0.84 80.4 yes View details
ndhG SSC 531 0.4922 0.84 79.1 yes View details
psaC-ndhD SSC 470 0.4939 0.87 78.6 yes View details
ndhD SSC 1164 0.4763 0.87 81.4 yes View details
ccsA SSC 993 0.4684 0.88 81.8 yes View details
trnL-UAG-ndhF SSC 1885 0.4601 0.78 78.1 yes View details
ndhF SSC 2238 0.4677 0.89 80.5 yes View details
petA-psbJ LSC 863 0.0457 0.99 79.9 yes View details
ndhI SSC 504 0.4431 0.80 77.4 yes View details
rps15-ndhH SSC 130 0.3984 0.95 77.2 yes View details
ndhI-ndhG SSC 395 0.3977 0.87 77.0 yes View details
ndhE-psaC SSC 325 0.4006 0.96 76.9 yes View details
ndhA-ndhI SSC 76 0.4853 0.89 75.8 yes View details
ndhE SSC 303 0.4704 0.89 75.7 yes View details
ndhG-ndhE SSC 121 0.4579 0.88 75.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petA-psbJ_p1 petA-psbJ CCCATTACGTGTCCAAGGAC CATATTCCGGATTGGGGTCA 1010 1.000 74.1
petA-psbJ_p2 petA-psbJ GACCCATTACGTGTCCAAGG CATATTCCGGATTGGGGTCA 1012 1.000 74.1
petA-psbJ_p3 petA-psbJ ACGTGTCCAAGGACTTTTGT CATATTCCGGATTGGGGTCA 1004 1.000 72.9
petA-psbJ_p4 petA-psbJ CCCATTACGTGTCCAAGGAC GCTGGTATTCTTGTGATCGGT 1056 1.000 72.8
petA-psbJ_p5 petA-psbJ GACCCATTACGTGTCCAAGG GCTGGTATTCTTGTGATCGGT 1058 1.000 72.8
ycf1_p1 ycf1 AGTGTCCCGTGTCAACTCTA CAACGTTTCAGCCTGGGATA 1051 0.500 59.1
ycf1_p2 ycf1 AGTGTCCCGTGTCAACTCTA AACGTTTCAGCCTGGGATAC 1050 0.500 59.1
ycf1_p3 ycf1 AAAGTGTCCCGTGTCAACTC CAACGTTTCAGCCTGGGATA 1053 0.500 58.7
ycf1_p4 ycf1 AAAGTGTCCCGTGTCAACTC AACGTTTCAGCCTGGGATAC 1052 0.500 58.7
ycf1_p5 ycf1 AGTGTCCCGTGTCAACTCTA AGCTGCTCGCCTTGTTAAAT 861 0.500 58.5
rps15-ndhH_p1 rps15-ndhH GCTGAAACGTTGTTGGTAGC TCCCAACGCGTTACATAAGG 1001 0.500 59.6
rps15-ndhH_p2 rps15-ndhH GCTGAAACGTTGTTGGTAGC CAGAAGCTCGTAGCATTGGT 1471 0.500 59.6
rps15-ndhH_p3 rps15-ndhH GCTGAAACGTTGTTGGTAGC GATGAGCCGAAGAACACCAT 876 0.500 59.5
rps15-ndhH_p4 rps15-ndhH GCTGAAACGTTGTTGGTAGC CCGAGCCATAACAAATGGGA 1145 0.500 59.3
rps15-ndhH_p5 rps15-ndhH GCTGAAACGTTGTTGGTAGC AACACCATGCATTGATGGGT 864 0.500 59.3
ndhH_p1 ndhH AAAAGATTTGTGCGTGTGCC ATTTCACCGAATCGCACGTA 2456 0.500 58.8
ndhH_p2 ndhH AAAAGATTTGTGCGTGTGCC TATTTCACCGAATCGCACGT 2457 0.500 58.8
ndhH_p3 ndhH AAAAGATTTGTGCGTGTGCC ACAAGGTGGTAGCCAAAAGG 2254 0.500 58.8
ndhH_p4 ndhH CTCAGAGAGGGTTGCGAAAA ATTTCACCGAATCGCACGTA 2014 0.500 58.6
ndhH_p5 ndhH CTCAGAGAGGGTTGCGAAAA TATTTCACCGAATCGCACGT 2015 0.500 58.6
ndhA-ndhI_p1 ndhA-ndhI TTTTGGGGGTGGAATCTGTG GTTGGGCAATACTCGACACA 909 0.500 58.4
ndhA-ndhI_p2 ndhA-ndhI TTTTGGGGGTGGAATCTGTG TGTTGGGCAATACTCGACAC 910 0.500 58.4
ndhA-ndhI_p3 ndhA-ndhI GGTTTTTGGGGGTGGAATCT GTTGGGCAATACTCGACACA 912 0.500 58.2
ndhA-ndhI_p4 ndhA-ndhI GGTTTTTGGGGGTGGAATCT TGTTGGGCAATACTCGACAC 913 0.500 58.2
ndhA-ndhI_p5 ndhA-ndhI CTCTAGCCGAGTGTGAGAGA GTTGGGCAATACTCGACACA 851 0.500 58.2
ndhI_p1 ndhI TTTTGGGGGTGGAATCTGTG CAATCCCAGCGAAAAAGCAG 1584 0.500 59.8
ndhI_p2 ndhI TTTTGGGGGTGGAATCTGTG TGACCCCTAAACCCCCTAAG 1540 0.500 59.7
ndhI_p3 ndhI GGTTTTTGGGGGTGGAATCT CAATCCCAGCGAAAAAGCAG 1587 0.500 59.7
ndhI_p4 ndhI CTCTAGCCGAGTGTGAGAGA CAATCCCAGCGAAAAAGCAG 1526 0.500 59.6
ndhI_p5 ndhI GGTTTTTGGGGGTGGAATCT TGACCCCTAAACCCCCTAAG 1543 0.500 59.6

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
Lomatogonium carinthiacum NC_086775.1 151796 View on NCBI ↗
Lomatogonium perenne NC_050659.1 151678 View on NCBI ↗