Markers + reference

Vittaria

2 species · Pteridaceae · Polypodiales

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Species 2
Genome length 150–151 kb
Candidate markers 259
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnD-GUC LSC 3067 0.3841 0.95 81.6 yes View details
ccsA SSC 954 0.4868 0.87 81.4 yes View details
ndhD SSC 1512 0.4985 0.86 81.0 yes View details
ndhE SSC 300 0.5152 0.99 73.5 yes View details
ndhG SSC 594 0.4639 0.89 81.7 yes View details
ndhI SSC 537 0.4798 0.83 78.9 yes View details
ndhH SSC 1185 0.4835 0.84 80.7 yes View details
rps15 SSC 270 0.5157 0.94 77.2 yes View details
ycf1 SSC 5136 0.4733 0.81 73.5 yes View details
chlN SSC 1392 0.4821 0.84 80.6 yes View details
chlL SSC 879 0.4160 0.80 79.5 yes View details
ndhF SSC 2181 0.4503 0.85 79.3 yes View details
rpl21 SSC 414 0.4674 0.89 78.1 yes View details
ndhA SSC 1912 0.4539 0.78 78.1 yes View details
trnR-ACG-rrn16 IRb 937 0.0365 0.91 78.0 yes View details
rrn16-trnR-ACG IRa 937 0.0365 0.91 78.0 yes View details
ycf1-chlN SSC 350 0.4551 0.92 77.6 yes View details
chlN-chlL SSC 76 0.4306 0.95 77.3 yes View details
ccsA-ndhD SSC 360 0.4352 0.90 77.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoB-trnD-GUC_p1 rpoB-trnD-GUC GGTGACACCTACCACGATTC GGCCTTTCTGCGGCTATTAT 817 0.500 59.1
rpoB-trnD-GUC_p2 rpoB-trnD-GUC GGTGACACCTACCACGATTC CGCTCCCAGATATCCCATTG 620 0.500 59.1
rpoB-trnD-GUC_p3 rpoB-trnD-GUC ACCATTCGAGGATACCGGAT GGCCTTTCTGCGGCTATTAT 584 0.500 59.1
rpoB-trnD-GUC_p4 rpoB-trnD-GUC ACCATTCGAGGATACCGGAT CGCTCCCAGATATCCCATTG 387 0.500 59.1
rpoB-trnD-GUC_p5 rpoB-trnD-GUC GGTGACACCTACCACGATTC AAGAGGTTTGTCTCAGGGGA 570 0.500 59.0
trnR-ACG-rrn16_p1 trnR-ACG-rrn16 GTGTGGTACGAAACTCCGTT CCAGGATCAAACTCTCCACG 978–1065 1.000 85.2
trnR-ACG-rrn16_p2 trnR-ACG-rrn16 AAGTGTGGTACGAAACTCCG CCAGGATCAAACTCTCCACG 980–1067 1.000 85.1
trnR-ACG-rrn16_p3 trnR-ACG-rrn16 GTGTGGTACGAAACTCCGTT CCACTGGAAACACCACTAGG 1052–1139 1.000 83.6
trnR-ACG-rrn16_p4 trnR-ACG-rrn16 AAGTGTGGTACGAAACTCCG CCACTGGAAACACCACTAGG 1054–1141 1.000 83.6
trnR-ACG-rrn16_p5 trnR-ACG-rrn16 GTGTGGTACGAAACTCCGTT GGAAACACCACTAGGATGCC 1047–1134 1.000 83.1
ndhF_p1 ndhF CGAATTGGAGCTTCGTGAGA TACCCAGGGAGAACCAACAT 2749 0.500 59.5
ndhF_p2 ndhF CTCCCAAGAGGCGTAGTAGA TACCCAGGGAGAACCAACAT 2911 0.500 59.1
ndhF_p3 ndhF GATCAACCTCACAATCCCCC TACCCAGGGAGAACCAACAT 2979 0.500 59.1
ndhF_p4 ndhF AATATGCAGGAGAGTCGGGA TACCCAGGGAGAACCAACAT 2779 0.500 58.9
ndhF_p5 ndhF CGAATTGGAGCTTCGTGAGA TTACCCAGGGAGAACCAACA 2750 0.500 58.5
rpl21_p1 rpl21 GCTAATAGCGGACATACGGG AAACTTCTTGAACGTCCGCT 1019 0.500 59.5
rpl21_p2 rpl21 GCTAATAGCGGACATACGGG AACTTCTTGAACGTCCGCTT 1018 0.500 59.5
rpl21_p3 rpl21 GCTAATAGCGGACATACGGG TGCGGAATATAGCGCAGTTT 1417 0.500 59.5
rpl21_p4 rpl21 GATCCTAACATTGACGCGGT AAACTTCTTGAACGTCCGCT 1379 0.500 59.1
rpl21_p5 rpl21 GATCCTAACATTGACGCGGT AACTTCTTGAACGTCCGCTT 1378 0.500 59.1
ccsA_p1 ccsA AAGCATCTCGGTTCGAATCC TTGCATTGCCAGGAATGAGT 1867 0.500 59.0
ccsA_p2 ccsA ATAGGTAGACACGCTGCTCT TTGCATTGCCAGGAATGAGT 1902 0.500 58.9
ccsA_p3 ccsA AAGCATCTCGGTTCGAATCC CCAGGAATGAGTGGCTTTGT 1859 0.500 58.9
ccsA_p4 ccsA ATAGGTAGACACGCTGCTCT CCAGGAATGAGTGGCTTTGT 1894 0.500 58.8
ccsA_p5 ccsA CAAGATGGGACGCTACCAAA TTGCATTGCCAGGAATGAGT 2199 0.500 58.6
ccsA-ndhD_p1 ccsA-ndhD TGTAAGCGCGACGTTGATTA TTGCATTGCCAGGAATGAGT 1254 0.500 59.3
ccsA-ndhD_p2 ccsA-ndhD TGTAAGCGCGACGTTGATTA TAAAATGGGCGGATATGGGC 1649 0.500 59.2
ccsA-ndhD_p3 ccsA-ndhD TGTAAGCGCGACGTTGATTA CCAGGAATGAGTGGCTTTGT 1246 0.500 59.2
ccsA-ndhD_p4 ccsA-ndhD CTTTTTGGAGTTGGGACCCA TTGCATTGCCAGGAATGAGT 919 0.500 58.8
ccsA-ndhD_p5 ccsA-ndhD TTGGAGTTGGGACCCAAAAG TTGCATTGCCAGGAATGAGT 915 0.500 58.8

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
Vittaria appalachiana NC_040219.1 149531 View on NCBI ↗
Vittaria graminifolia NC_040217.1 151035 View on NCBI ↗