Markers + reference

Asplenium

12 species · Aspleniaceae · Polypodiales

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Species 12
Genome length 149–157 kb
Candidate markers 264
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 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 Genome 1079 0.0978 0.99 85.3 yes View details
psbM-petN Genome 1209 0.1104 0.97 80.5 yes View details
trnC-GCA-trnG-GCC Genome 421 0.1224 0.95 78.3 yes View details
psbD-trnT-GGU Genome 1085 0.1006 0.98 81.3 yes View details
trnT-GGU-trnfM-CAU Genome 473 0.1484 0.97 77.6 yes View details
ndhC-trnM-CAU Genome 1129 0.1316 0.98 82.2 yes View details
petA-psbJ Genome 2569 0.1310 0.25 67.2 yes View details
ndhF Genome 2238 0.0829 0.99 79.6 yes View details
rpl32-trnP-GGG Genome 612 0.1761 0.98 80.3 yes View details
ccsA-ndhD Genome 850 0.1583 0.41 68.5 yes View details
rrn16-rps12 Genome 1213 0.0510 1.00 86.5 yes View details
rps12-rrn16 Genome 1213 0.0512 1.00 86.5 yes View details
petB Genome 1476 0.0615 0.99 84.5 yes View details
rpl20-rps12 Genome 994 0.0757 0.99 82.9 yes View details
matK-rps16 Genome 646 0.1110 1.00 81.8 yes View details
psbE-petL Genome 787 0.0914 0.99 81.5 yes View details
ndhB Genome 1183 0.0866 0.98 81.4 yes View details
psbK-psbI Genome 591 0.1056 0.98 81.1 yes View details
trnW-CCA-trnP-UGG Genome 161 0.1213 1.00 80.9 yes View details
ndhB Genome 738 0.0678 1.00 76.2 no 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
ndhB_p1 ndhB ACGAAGGATCAAGCTCACTA GAAGCAGAGAGAGGCAAGTC 229–240 0.250 45.6
ndhB_p2 ndhB TACGAAGGATCAAGCTCACT GAAGCAGAGAGAGGCAAGTC 230–241 0.250 45.6
ndhB_p3 ndhB ACGAAGGATCAAGCTCACTA GAAATCAACTCTTGCCGTGC 288–298 0.250 43.8
ndhB_p4 ndhB ACGAAGGATCAAGCTCACTA ACTAGGGCAATGGAAGGTCT 939–949 0.250 40.5
ndhB_p5 ndhB TACGAAGGATCAAGCTCACT ACTAGGGCAATGGAAGGTCT 940–950 0.250 40.5
matK-rps16_p1 matK-rps16 GTCGACGAATTAAGCGGACT CTGTGTGCACTCACCTATCC 1396–1439 0.750 78.6
matK-rps16_p2 matK-rps16 TCGACGAATTAAGCGGACTG CTGTGTGCACTCACCTATCC 1395–1438 0.750 78.6
matK-rps16_p3 matK-rps16 GTCGACGAATTAAGCGGACT CCTGTGTGCACTCACCTATC 1397–1440 0.667 75.3
matK-rps16_p4 matK-rps16 CGACGAATTAAGCGGACTGA CTGTGTGCACTCACCTATCC 1399–1437 0.583 72.0
matK-rps16_p5 matK-rps16 CGACGAATTAAGCGGACTGA CCTGTGTGCACTCACCTATC 1400–1438 0.500 68.2
rps16_p1 rps16 GCTGGCCCCATTAGATTCTC AAGACCATACCGAGGTTGGA 1702–1721 0.667 77.2
rps16_p2 rps16 GCTGGCCCCATTAGATTCTC CGAAGACCATACCGAGGTTG 1704–1723 0.667 77.0
rps16_p3 rps16 GCTGGCCCCATTAGATTCTC ACAACAGCTCGTATCGAACC 1679–1698 0.250 56.4
rps16_p4 rps16 GTTGTAAGCTGGCCCCATTA ACAACAGCTCGTATCGAACC 1686–1705 0.250 56.1
rps16_p5 rps16 CTCCGGATCATGCCTAACAG ACAACAGCTCGTATCGAACC 1875 0.083 42.0
psbK-psbI_p1 psbK-psbI GGGGAAAAGTCTTGCACTGA GAATCCCTCTCTCTCCCCTC 1526 0.083 43.1
psbK-psbI_p2 psbK-psbI GGGGAAAAGTCTTGCACTGA ACTTGGTTTTGAGCGGAACT 2053 0.083 42.8
psbK-psbI_p3 psbK-psbI GGGGAAAAGTCTTGCACTGA GAGAGATGGCTGAGAGGTCT 1596 0.083 42.6
psbK-psbI_p4 psbK-psbI GGGGAAAAGTCTTGCACTGA TTCGAATCCCTCTCTCTCCC 1529 0.083 42.6
psbK-psbI_p5 psbK-psbI GATTCGAACCTCCGAGTGAC GAATCCCTCTCTCTCCCCTC 1376 0.083 42.5
psbM-petN_p1 psbM-petN TCTCTACATTCAAACGGCCG AAGACGGAGGACTGCAAATC 1768–1925 1.000 91.2
psbM-petN_p2 psbM-petN TCTCTACATTCAAACGGCCG TAGTCAAGCGGTAAGACGGA 1780–1937 1.000 90.6
psbM-petN_p3 psbM-petN TCTCTACATTCAAACGGCCG TGTCTCAATTCGTCACGCAT 1655–1695 0.250 58.6
psbM-petN_p4 psbM-petN TCTCTACATTCAAACGGCCG TGTGAAAGTGTGAAAGGCGA 1919–1959 0.250 58.4
psbM-petN_p5 psbM-petN TCTAAACGATGGGGGCTTTG TGTGAAAGTGTGAAAGGCGA 2440–2473 0.250 57.2
trnC-GCA-trnG-GCC_p1 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GTTCGATTCCCGCTATCCG 415–495 1.000 81.7
trnC-GCA-trnG-GCC_p2 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGGTTCGATTCCCGCTATC 417–497 1.000 81.5
trnC-GCA-trnG-GCC_p3 trnC-GCA-trnG-GCC GATTTGCAGTCCTCCGTCTT GGTTCGATTCCCGCTATCC 416–496 1.000 81.5
trnC-GCA-trnG-GCC_p4 trnC-GCA-trnG-GCC TCCGTCTTACCGCTTGACTA GTTCGATTCCCGCTATCCG 403–483 1.000 81.1
trnC-GCA-trnG-GCC_p5 trnC-GCA-trnG-GCC TCCGTCTTACCGCTTGACTA GGTTCGATTCCCGCTATCC 404–484 1.000 80.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Asplenium antiquum OR764773.1 150690 View on NCBI ↗
Asplenium castaneoviride NC_071922.1 153071 View on NCBI ↗
Asplenium incisum NC_071921.1 153116 View on NCBI ↗
Asplenium komarovii MZ064529.1 149393 View on NCBI ↗
Asplenium nidus NC_045119.1 156173 View on NCBI ↗
Asplenium pekinense NC_035837.1 152479 View on NCBI ↗
Asplenium prolongatum NC_035838.1 151115 View on NCBI ↗
Asplenium pseudocapillipes NC_080354.1 157242 View on NCBI ↗
Asplenium ruprechtii NC_071923.1 153066 View on NCBI ↗
Asplenium scolopendrium var. americanum MZ329814.1 149344 View on NCBI ↗
Asplenium scolopendrium var. scolopendrium MZ329815.1 149379 View on NCBI ↗
Asplenium speluncae PX977812.1 155362 View on NCBI ↗