Markers + reference

Isoetes

53 species · Isoetaceae · Isoetales

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Species 53
Genome length 143–146 kb
Candidate markers 266
Primer pairs 85

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 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbJ-petA Genome 1325 0.0373 0.98 72.8 yes View details
rbcL-atpB Genome 831 0.0568 0.94 74.6 yes View details
trnT-GGU-trnE-UUC Genome 1315 0.0385 0.99 72.4 yes View details
trnK-UUU-chlB Genome 1506 0.0354 0.98 68.8 yes View details
psbM-trnL-CAA Genome 505 0.0492 0.98 69.4 yes View details
ndhF-chlN Genome 936 0.0615 0.98 74.7 yes View details
ycf2 Genome 6362 0.0324 0.99 66.8 yes View details
trnP-GGG-rpl32 Genome 361 0.0515 1.00 73.7 yes View details
trnV-UAC-ndhC Genome 947 0.0299 0.98 70.0 yes View details
psaI-trnR-CCG Genome 1694 0.0336 0.99 68.6 yes View details
psbB-clpP Genome 1115 0.0295 0.99 67.7 yes View details
psaJ-trnP-UGG Genome 669 0.0293 0.99 67.2 yes View details
petL-psbE Genome 1815 0.0324 0.97 67.0 yes View details
trnF-GAA-trnL-UAA Genome 510 0.0407 0.99 67.0 yes View details
ccsA-trnL-UAG Genome 187 0.0457 1.00 67.0 yes View details
psbD-trnT-GGU Genome 1333 0.0307 0.99 66.6 yes View details
psbK-psbI Genome 382 0.0343 0.98 65.6 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
psbB-clpP_p1 psbB-clpP ATACTCCAACCACCCCATGA AGTCGCACTGTACGTCAATC 993–1487 1.000 91.7
psbB-clpP_p2 psbB-clpP TGATACTCCAACCACCCCAT AGTCGCACTGTACGTCAATC 995–1489 1.000 91.7
psbB-clpP_p3 psbB-clpP GGTTGTGCTTCTCCAGTCAA AGTCGCACTGTACGTCAATC 1293–1787 1.000 91.5
psbB-clpP_p4 psbB-clpP TTGTGCTTCTCCAGTCAACC AGTCGCACTGTACGTCAATC 1291–1785 1.000 91.5
psbB-clpP_p5 psbB-clpP AGAAACTAACGCTGTGTGCA AGTCGCACTGTACGTCAATC 847–1341 1.000 91.4
psaJ-trnP-UGG_p1 psaJ-trnP-UGG AGGCGCTGTGGAAAGATATG CGAACTGAACTAAGAGCGCT 924–991 1.000 91.5
psaJ-trnP-UGG_p2 psaJ-trnP-UGG CAGGCGCTGTGGAAAGATAT CGAACTGAACTAAGAGCGCT 925–992 1.000 91.5
psaJ-trnP-UGG_p3 psaJ-trnP-UGG CACGAACCTCCCCAATACTG CGAACTGAACTAAGAGCGCT 1512–1578 0.925 88.7
psaJ-trnP-UGG_p4 psaJ-trnP-UGG CACGAACCTCCCCAATACTG GGAGACCTACGTTCTACCGA 1529–1595 0.925 88.5
psaJ-trnP-UGG_p5 psaJ-trnP-UGG TCACGAACCTCCCCAATACT CGAACTGAACTAAGAGCGCT 1513–1579 0.925 88.4
petL-psbE_p1 petL-psbE AAAGCTGGAGTTAGAGCAGC CTCTCCCGTATTCCCAGACA 1420–1892 1.000 89.4
petL-psbE_p2 petL-psbE AAAGCTGGAGTTAGAGCAGC TCTCCCGTATTCCCAGACAT 1419–1891 1.000 87.4
petL-psbE_p3 petL-psbE CTGGAGTTAGAGCAGCCAAT CTCTCCCGTATTCCCAGACA 1416–1888 1.000 84.6
petL-psbE_p4 petL-psbE AAAGCTGGAGTTAGAGCAGC AATAATGTCGGCGAAAGGGC 1441–1913 1.000 83.3
petL-psbE_p5 petL-psbE CTGGAGTTAGAGCAGCCAAT TCTCCCGTATTCCCAGACAT 1415–1887 1.000 82.6
psbJ-petA_p1 psbJ-petA ATGGCCCATACTCCGGATTA TCCTCCTGATCGTATTCCCC 1967–2062 0.981 90.8
psbJ-petA_p2 psbJ-petA TACGGTTTTCTCCCCAGGAT TCCTCCTGATCGTATTCCCC 2370–2465 0.981 90.8
psbJ-petA_p3 psbJ-petA CCCATACTCCGGATTAGGGT CGTCCGGTGGTTGATATTGT 1614–1695 0.434 67.5
psbJ-petA_p4 psbJ-petA CCCATACTCCGGATTAGGGT TCTTTCACCAGACCCTGCTA 1825–1906 0.434 66.8
psbJ-petA_p5 psbJ-petA CCCATACTCCGGATTAGGGT TCCTCCTGATCGTATTCCCC 1963–2044 0.434 66.3
psaI-trnR-CCG_p1 psaI-trnR-CCG TCGTTGCGGATGAAGAAACA CATTCACTCCGGTACTGTGG 2494–2719 0.698 78.8
psaI-trnR-CCG_p2 psaI-trnR-CCG TTGAACTCGTTGCGGATGAA CATTCACTCCGGTACTGTGG 2500–2725 0.698 78.8
psaI-trnR-CCG_p3 psaI-trnR-CCG TTTGAACTCGTTGCGGATGA CATTCACTCCGGTACTGTGG 2501–2726 0.698 78.8
psaI-trnR-CCG_p4 psaI-trnR-CCG CCATTCGGATTGCCAATTCG CATTCACTCCGGTACTGTGG 2782–2999 0.604 75.0
psaI-trnR-CCG_p5 psaI-trnR-CCG TAAGCCATTCGGATTGCCAA CATTCACTCCGGTACTGTGG 2786–2998 0.566 73.4
rbcL-atpB_p1 rbcL-atpB TCTCTCCAACGCATAAACGG CGTCCAAGAGTAGCTTCACC 1787–1833 1.000 91.9
rbcL-atpB_p2 rbcL-atpB TGACCCTTAATCTCACCCGT CGTCCAAGAGTAGCTTCACC 1853–1899 1.000 91.6
rbcL-atpB_p3 rbcL-atpB ACCTTCCTCGAACAGATCCA CGTCCAAGAGTAGCTTCACC 1473–1519 1.000 91.5
rbcL-atpB_p4 rbcL-atpB GCTTTGAATCCAACACTCGC CGTCCAAGAGTAGCTTCACC 1184–1230 0.830 84.9
rbcL-atpB_p5 rbcL-atpB CGGTCTCTCCAACGCATAAA CGTCCAAGAGTAGCTTCACC 1790–1836 0.679 79.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (53)

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

Species Accession Length (bp) Link
Isoetes aequinoctialis NC_069317.1 143671 View on NCBI ↗
Isoetes amazonica MW255547.1 143339 View on NCBI ↗
Isoetes anamariae MW255541.1 143252 View on NCBI ↗
Isoetes australis NC_069336.1 143237 View on NCBI ↗
Isoetes azorica NC_069326.1 144936 View on NCBI ↗
Isoetes baodongii NC_086815.1 145494 View on NCBI ↗
Isoetes biafrana NC_069320.1 143629 View on NCBI ↗
Isoetes bolanderi MZ603743.1 144991 View on NCBI ↗
Isoetes butleri NC_038071.1 144912 View on NCBI ↗
Isoetes cangae NC_039392.1 143380 View on NCBI ↗
Isoetes changleensis OM281828.1 145494 View on NCBI ↗
Isoetes cipoensis MW255545.1 143330 View on NCBI ↗
Isoetes cubana NC_069334.1 143143 View on NCBI ↗
Isoetes drummondii NC_069328.1 145279 View on NCBI ↗
Isoetes duriei NC_069321.1 144291 View on NCBI ↗
Isoetes echinospora NC_069325.1 144998 View on NCBI ↗
Isoetes engelmannii NC_038080.1 144817 View on NCBI ↗
Isoetes flaccida NC_014675.1 145303 View on NCBI ↗
Isoetes flaccida var. chapmanii MG599108.1 145096 View on NCBI ↗
Isoetes flaccida var. flaccida MG668893.1 145126 View on NCBI ↗
Isoetes gardneriana MW255548.1 143326 View on NCBI ↗
Isoetes giessii NC_069318.1 143699 View on NCBI ↗
Isoetes graniticola NC_039821.1 145118 View on NCBI ↗
Isoetes harleyi MW255546.1 142880 View on NCBI ↗
Isoetes lechleri NC_069322.1 144964 View on NCBI ↗
Isoetes longifolia MW255543.1 143308 View on NCBI ↗
Isoetes luetzelburgii MW255544.1 143346 View on NCBI ↗
Isoetes malinverniana NC_040924.1 145535 View on NCBI ↗
Isoetes maritima MZ603747.1 145097 View on NCBI ↗
Isoetes mattaponica NC_039703.1 145065 View on NCBI ↗
Isoetes melanopoda subsp. melanopoda MG668895.1 145075 View on NCBI ↗
Isoetes melanopoda subsp. silvatica MG668896.1 145109 View on NCBI ↗
Isoetes melanospora NC_038072.1 145045 View on NCBI ↗
Isoetes neoguineensis NC_069330.1 145411 View on NCBI ↗
Isoetes nigritiana NC_069331.1 143221 View on NCBI ↗
Isoetes nuttallii NC_038073.1 144680 View on NCBI ↗
Isoetes occidentalis NC_069324.1 144912 View on NCBI ↗
Isoetes orientalis NC_065385.1 145501 View on NCBI ↗
Isoetes pallida NC_069335.1 143173 View on NCBI ↗
Isoetes panamensis MW255549.1 143331 View on NCBI ↗
Isoetes piedmontana NC_040925.1 145030 View on NCBI ↗
Isoetes pusilla NC_069327.1 145224 View on NCBI ↗
Isoetes sampathkumaranii NC_069329.1 144947 View on NCBI ↗
Isoetes schweinfurthii NC_069333.1 143220 View on NCBI ↗
Isoetes serracarajensis NC_039393.1 143380 View on NCBI ↗
Isoetes smithii NC_069323.1 144865 View on NCBI ↗
Isoetes transvaalensis NC_069319.1 143698 View on NCBI ↗
Isoetes triangula MW255550.1 143357 View on NCBI ↗
Isoetes valida NC_038074.1 145132 View on NCBI ↗
Isoetes welwitschii NC_069332.1 143215 View on NCBI ↗
Isoetes x herb-wagneri MZ603750.1 144975 View on NCBI ↗
Isoetes yuhangensis OM281829.1 145501 View on NCBI ↗
Isoetes yunguiensis NC_041146.1 145355 View on NCBI ↗