Markers + reference

Ophioglossum

3 species · Ophioglossaceae · Ophioglossales

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Species 3
Genome length 138–139 kb
Candidate markers 268
Primer pairs 85

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-CAA-ycf2 Genome 1578 0.0059 1.00 55.5 yes View details
atpF Genome 1291 0.0021 1.00 47.6 yes View details
rpoC1 Genome 2851 0.0000 1.00 22.4 yes View details
rpoB Genome 3189 0.0002 1.00 29.6 yes View details
psbD-trnT-GGU Genome 737 0.0018 1.00 47.4 yes View details
rps8 Genome 399 0.0017 1.00 39.8 yes View details
rps8-rpl14 Genome 345 0.0039 1.00 57.9 yes View details
rpl16 Genome 1192 0.0017 1.00 47.9 yes View details
rpoC1-rpoB Genome 26 0.0256 1.00 56.3 yes View details
petN-psbM Genome 628 0.0011 1.00 46.9 yes View details
petA-psbJ Genome 641 0.0010 1.00 46.9 yes View details
rpl20-rps12 Genome 645 0.0010 1.00 46.9 yes View details
ccsA Genome 954 0.0007 1.00 46.7 yes View details
atpA Genome 1527 0.0004 1.00 46.5 yes View details
rpl2 Genome 1515 0.0004 1.00 46.5 yes View details
ndhD Genome 1497 0.0004 1.00 46.5 yes View details
psaC-ndhE Genome 65 0.0103 1.00 46.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnL-CAA-ycf2_p1 trnL-CAA-ycf2 ACAGCTTGGAGGTTCGAATC TGAAGATATCTTTTCCGGTTGA 1632–1912 1.000 45.3
trnL-CAA-ycf2_p2 trnL-CAA-ycf2 ATTGAGTGCCTTGATGGTGG TGAAGATATCTTTTCCGGTTGA 1688–1968 1.000 44.8
trnL-CAA-ycf2_p3 trnL-CAA-ycf2 CACAGCTTGGAGGTTCGAAT TGAAGATATCTTTTCCGGTTGA 1633–1913 1.000 44.6
trnL-CAA-ycf2_p4 trnL-CAA-ycf2 AACGGTAAACACGCGAGATT TGAAGATATCTTTTCCGGTTGA 1668–1948 1.000 44.6
trnL-CAA-ycf2_p5 trnL-CAA-ycf2 CGGAATGGAATTGAGTGCCT TGAAGATATCTTTTCCGGTTGA 1697–1977 1.000 44.6
atpA_p1 atpA CCACAGATTCCAGGAACCAC ACCATGAAAAGCACGACTGA 1644 1.000 76.6
atpA_p2 atpA CCACAGATTCCAGGAACCAC GGAACCATGAAAAGCACGAC 1647 1.000 76.0
atpA_p3 atpA CCACAGATTCCAGGAACCAC TATCACATTGGCTTGCTCGG 1665 1.000 76.0
atpA_p4 atpA CCACAGATTCCAGGAACCAC CTCGGAACCATGAAAAGCAC 1650 1.000 73.7
atpA_p5 atpA CACAGATTCCAGGAACCACA ACCATGAAAAGCACGACTGA 1643 1.000 73.5
atpF_p1 atpF AACTACCGATCTCGTCAGGT TTTGAGCGGGATTCCTGAAG 1440 1.000 78.3
atpF_p2 atpF ACTCCTCGATTTGTTTGCGA TTTGAGCGGGATTCCTGAAG 1464 1.000 78.0
atpF_p3 atpF ACTACCGATCTCGTCAGGTC TTTGAGCGGGATTCCTGAAG 1439 1.000 76.6
atpF_p4 atpF AACTACCGATCTCGTCAGGT GAGCGGGATTCCTGAAGAAA 1437 1.000 76.0
atpF_p5 atpF ACTCCTCGATTTGTTTGCGA GAGCGGGATTCCTGAAGAAA 1461 1.000 75.7
rpoC1_p1 rpoC1 GCCATCGTGAAAACCTCGAA GAAAAGCGACGGATGTTTGA 2998 1.000 65.6
rpoC1_p2 rpoC1 GCCATCGTGAAAACCTCGAA AGAAAAGCGACGGATGTTTG 2999 1.000 65.5
rpoC1_p3 rpoC1 TCTGCCATCGTGAAAACCTC AAAAGCGACGGATGTTTGAT 3000 1.000 65.2
rpoC1_p4 rpoC1 ACCTCGAAAATTCTGTGAGCA GAAAAGCGACGGATGTTTGA 2986 1.000 63.3
rpoC1_p5 rpoC1 ACCTCGAAAATTCTGTGAGCA AGAAAAGCGACGGATGTTTG 2987 1.000 63.3
rpoC1-rpoB_p1 rpoC1-rpoB GTTCGGGAGATGCTAACTGG CCGGGAATTACGGTCGTTAG 166 1.000 78.8
rpoC1-rpoB_p2 rpoC1-rpoB GTTCGGGAGATGCTAACTGG GGTCGTTAGCTCCGAATCTG 155 1.000 78.8
rpoC1-rpoB_p3 rpoC1-rpoB TCGGGAGATGCTAACTGGAT CCGGGAATTACGGTCGTTAG 164 1.000 78.5
rpoC1-rpoB_p4 rpoC1-rpoB TCGGGAGATGCTAACTGGAT GGTCGTTAGCTCCGAATCTG 153 1.000 78.5
rpoC1-rpoB_p5 rpoC1-rpoB TTCGGGAGATGCTAACTGGA CCGGGAATTACGGTCGTTAG 165 1.000 78.1
rpoB_p1 rpoB ACCACCTTATGCATGGTTTG GATCGGGACAAATTGGTCGA 262 1.000 66.4
rpoB_p2 rpoB ACCACCTTATGCATGGTTTG TCAACAAAGGTGTGGATCGG 276 1.000 65.7
rpoB_p3 rpoB ACCACCTTATGCATGGTTTG TGGATCGGGACAAATTGGTC 264 1.000 65.6
rpoB_p4 rpoB ACCACCTTATGCATGGTTTG GGTGTGGATCGGGACAAATT 268 1.000 65.2
rpoB_p5 rpoB ACCACCTTATGCATGGTTTG GTGGATCGGGACAAATTGGT 265 1.000 65.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Ophioglossum californicum NC_020147.1 138270 View on NCBI ↗
Ophioglossum thermale NC_088530.1 138537 View on NCBI ↗
Ophioglossum vulgatum MZ066610.1 138562 View on NCBI ↗