Markers + reference

Eranthis

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 159–160 kb
Candidate markers 266
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5607 0.2764 0.85 74.6 yes View details
ndhH SSC 1182 0.4632 0.82 79.8 yes View details
ndhA SSC 1994 0.4792 0.81 78.6 yes View details
ndhG SSC 534 0.5086 0.87 80.0 yes View details
ndhD SSC 1503 0.4745 0.81 79.6 yes View details
ndhF SSC 2232 0.4657 0.80 77.9 yes View details
ycf1 IRa 2892 0.0370 1.00 62.2 no View details
trnG-UCC-trnR-UCU LSC 169 0.0750 0.95 81.0 yes View details
ccsA SSC 972 0.4491 0.83 80.2 yes View details
trnL-UAG-ndhF SSC 1160 0.4455 0.83 80.2 yes View details
ndhD-ccsA SSC 253 0.4958 0.95 77.3 yes View details
ndhG-ndhE SSC 257 0.4156 0.95 77.2 yes View details
ndhE SSC 306 0.4097 0.94 77.2 yes View details
rpl14-rpl16 LSC 142 0.0945 0.89 77.1 yes View details
rps15-ndhH SSC 177 0.3976 0.94 77.0 yes View details
ndhE-psaC SSC 257 0.4750 0.93 76.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAACAAATTGCGTCCAA 287–296 1.000 75.5
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAACAAATTGCGTCCAA 290–299 1.000 75.2
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGGAAACAAATTGCGTCCAA 291–300 1.000 73.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT TGGAAACAAATTGCGTCCAA 276–285 1.000 72.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU TGACGTCGACTATAACCCCT TGGAAACAAATTGCGTCCAA 307–316 1.000 71.9
rpl14-rpl16_p1 rpl14-rpl16 CGCTGTTGTCCGCTACATTT GCGTCCAAAATGCCTATACG 218–230 1.000 73.3
rpl14-rpl16_p2 rpl14-rpl16 CGCTGTTGTCCGCTACATT GCGTCCAAAATGCCTATACG 218–230 1.000 70.6
rpl14-rpl16_p3 rpl14-rpl16 CGCTGTTGTCCGCTACATTT ATAGCTGCGTCCAAAATGCC 224–236 1.000 68.5
rpl14-rpl16_p4 rpl14-rpl16 CGCTGTTGTCCGCTACATTT GCTGCGTCCAAAATGCCTAT 221–233 1.000 68.5
rpl14-rpl16_p5 rpl14-rpl16 CGCTGTTGTCCGCTACATTT CTATAGCTGCGTCCAAAATGC 226–238 1.000 68.4
ycf1_p1 ycf1 TGCACCAAACCATAGCTGTT GACATACTGAAACGACTCCCA 445 0.500 47.2
ycf1_p2 ycf1 TGCACCAAACCATAGCTGTT TGACATACTGAAACGACTCCC 446 0.500 47.2
ycf1_p3 ycf1 TGATTATTGAACCAGCCCGG GACATACTGAAACGACTCCCA 496 0.500 46.9
ycf1_p4 ycf1 TGATTATTGAACCAGCCCGG TGACATACTGAAACGACTCCC 497 0.500 46.9
ycf1_p5 ycf1 ACACCATCCAGTGCAAAGAG GACATACTGAAACGACTCCCA 885 0.500 46.5
rps15-ndhH_p1 rps15-ndhH TCGGGAGCTCAAAATTCGTT CCTCTCCACCAATAATGCCC 836 0.500 58.5
rps15-ndhH_p2 rps15-ndhH TTCGGGAGCTCAAAATTCGT CCTCTCCACCAATAATGCCC 837 0.500 58.5
rps15-ndhH_p3 rps15-ndhH TCGGGAGCTCAAAATTCGTT CCCCTTCAACTCGTTCCAAA 815 0.500 58.4
rps15-ndhH_p4 rps15-ndhH TTCGGGAGCTCAAAATTCGT CCCCTTCAACTCGTTCCAAA 816 0.500 58.4
rps15-ndhH_p5 rps15-ndhH TCGGGAGCTCAAAATTCGTT ATCCAGCCATAGGGGAGATC 714 0.500 58.3
ndhH_p1 ndhH TCGGGAGCTCAAAATTCGTT ACCCCTATACTGAGATCGGC 1774 0.500 58.0
ndhH_p2 ndhH TTCGGGAGCTCAAAATTCGT ACCCCTATACTGAGATCGGC 1775 0.500 58.0
ndhH_p3 ndhH TCGGGAGCTCAAAATTCGTT ATACGTTGTTGTACCCCTGC 1567 0.500 57.7
ndhH_p4 ndhH TTCGGGAGCTCAAAATTCGT ATACGTTGTTGTACCCCTGC 1568 0.500 57.7
ndhH_p5 ndhH TCGGGAGCTCAAAATTCGTT CAACGAATCGCACGTAGAGA 1948 0.500 57.7
ndhA_p1 ndhA ACCTTCGCCCACTTTTGAAT CGCCCCAAAGCAATTTGATT 2745 0.500 59.2
ndhA_p2 ndhA ACCTTCGCCCACTTTTGAAT CTCACCACCCCATAGTTTGG 2941 0.500 58.9
ndhA_p3 ndhA CAGGCTCTGGAAGGAATTCC CGCCCCAAAGCAATTTGATT 2858 0.500 58.8
ndhA_p4 ndhA CGATCGGAGTGTTTTTCCCT CGCCCCAAAGCAATTTGATT 2658 0.500 58.5
ndhA_p5 ndhA ACCTTCGCCCACTTTTGAAT GACCGATATACCTTGCAGCC 2384 0.500 58.3

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
Eranthis byunsanensis NC_066652.1 160324 View on NCBI ↗
Eranthis stellata NC_041536.1 159251 View on NCBI ↗