Markers + reference

Anthurium

2 species · Araceae · Alismatales

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Species 2
Genome length 163–163 kb
Candidate markers 257
Primer pairs 90

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 8 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2238 0.4631 0.77 77.1 yes View details
rpl32-trnL-UAG SSC 721 0.4653 0.90 82.2 yes View details
ccsA SSC 972 0.4514 0.84 80.6 yes View details
ndhD SSC 1500 0.4728 0.89 82.0 yes View details
psaC-ndhE SSC 1566 0.4410 0.94 83.0 yes View details
ndhI SSC 543 0.4697 0.88 80.5 yes View details
ndhA SSC 2183 0.4399 0.75 76.9 yes View details
ndhH SSC 1182 0.4775 0.88 81.8 yes View details
rps15 SSC 279 0.5254 0.99 73.5 yes View details
ycf1 SSC 5685 0.4447 0.83 74.1 yes View details
trnN-GUU-ndhF SSC 1089 0.2889 0.92 82.6 yes View details
ndhF-rpl32 SSC 1240 0.4343 0.90 82.3 yes View details
ndhG-ndhI SSC 705 0.3265 0.90 82.2 yes View details
rps15-ycf1 SSC 1002 0.4413 0.82 79.9 yes View details
ndhI-ndhA SSC 93 0.5000 0.97 75.8 yes View details
psaC SSC 246 0.4507 0.87 75.0 yes View details
ndhE-ndhG SSC 386 0.4348 0.77 74.4 yes View details
ndhH-rps15 SSC 104 0.4659 0.85 74.4 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnN-GUU-ndhF_p1 trnN-GUU-ndhF CCTGGCCCAAATCAGCATAT AAAGGTCGTAACTGGGGGTA 1817 0.500 59.7
trnN-GUU-ndhF_p2 trnN-GUU-ndhF ACCTGGGGCTTTTTACAAGG AAAGGTCGTAACTGGGGGTA 1585 0.500 59.7
trnN-GUU-ndhF_p3 trnN-GUU-ndhF CGGGAGAATTGATGACTGCA AAAGGTCGTAACTGGGGGTA 1663 0.500 59.5
trnN-GUU-ndhF_p4 trnN-GUU-ndhF AACGGTAAAAACGAGCCCTT AAAGGTCGTAACTGGGGGTA 1447 0.500 59.5
trnN-GUU-ndhF_p5 trnN-GUU-ndhF ACGGTAAAAACGAGCCCTTT AAAGGTCGTAACTGGGGGTA 1446 0.500 59.5
ndhF_p1 ndhF TGACTTCATTTTTCACTTTTT ATTAGCGGATACTGGGTCCA 2736 0.500 20.0
ndhF_p2 ndhF TGACTTCATTTTTCACTTTTT TTAGCGGATACTGGGTCCAT 2735 0.500 20.0
ndhF_p3 ndhF TTGACTTCATTTTTCACTTTT ATTAGCGGATACTGGGTCCA 2737 0.500 20.0
ndhF_p4 ndhF TTGACTTCATTTTTCACTTTT TTAGCGGATACTGGGTCCAT 2736 0.500 20.0
ndhF_p5 ndhF TTTGACTTCATTTTTCACTTT TTAGCGGATACTGGGTCCAT 2737 0.500 20.0
ndhF-rpl32_p1 ndhF-rpl32 CTGCAATTGGTCGTGTGAAC TACTCGTTTGGTCGCACAAA 1912 0.500 59.2
ndhF-rpl32_p2 ndhF-rpl32 CTGCAATTGGTCGTGTGAAC TTACTCGTTTGGTCGCACAA 1913 0.500 59.2
ndhF-rpl32_p3 ndhF-rpl32 AATAGGGAGGCACACAGAGT TACTCGTTTGGTCGCACAAA 2096 0.500 59.2
ndhF-rpl32_p4 ndhF-rpl32 AATAGGGAGGCACACAGAGT TTACTCGTTTGGTCGCACAA 2097 0.500 59.2
ndhF-rpl32_p5 ndhF-rpl32 AGGAAAAGCCCACATACGAC TACTCGTTTGGTCGCACAAA 1527 0.500 58.6
rpl32-trnL-UAG_p1 rpl32-trnL-UAG TTGTGCGACCAAACGAGTAA AGCGTGTCTACCGATTTCAC 770 0.500 59.4
rpl32-trnL-UAG_p2 rpl32-trnL-UAG TTTGTGCGACCAAACGAGTA AGCGTGTCTACCGATTTCAC 771 0.500 59.4
rpl32-trnL-UAG_p3 rpl32-trnL-UAG TTGTGCGACCAAACGAGTAA CAGCGTGTCTACCGATTTCA 771 0.500 59.4
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TTTGTGCGACCAAACGAGTA CAGCGTGTCTACCGATTTCA 772 0.500 59.4
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TTGTGCGACCAAACGAGTAA GCACTTGGTGTGGTTATTGC 1224 0.500 59.0
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT TTGCATTGCCAGGAATGAGT 1619 0.500 59.4
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG TTGCATTGCCAGGAATGAGT 1618 0.500 59.3
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT CATTGCCAGGAATGAGTGGT 1616 0.500 58.7
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG CATTGCCAGGAATGAGTGGT 1615 0.500 58.7
ccsA_p5 ccsA GTGAAATCGGTAGACACGCT CTTCTCTTGCATTGCCAGGA 1625 0.500 58.6
ndhD_p1 ndhD TCTCTCTGGAGCAGTATGGG GAACCGAAGATTGCGTAGGT 2146 0.500 59.3
ndhD_p2 ndhD TCTCTCTGGAGCAGTATGGG TATGGCATGAGACAACTCGC 2071 0.500 58.9
ndhD_p3 ndhD AATGAGGCATGGGGATCCTA GAACCGAAGATTGCGTAGGT 2124 0.500 58.8
ndhD_p4 ndhD TAATGAGGCATGGGGATCCT GAACCGAAGATTGCGTAGGT 2125 0.500 58.8
ndhD_p5 ndhD TGAGGCATGGGGATCCTATT GAACCGAAGATTGCGTAGGT 2122 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
Anthurium andraeanum NC_072558.1 162560 View on NCBI ↗
Anthurium huixtlense NC_051870.1 163116 View on NCBI ↗