Markers + reference

Ilex

101 species · Aquifoliaceae · Aquifoliales

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Species 101
Genome length 157–158 kb
Candidate markers 285
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 285 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 430 0.0249 0.84 71.9 yes View details
rps16-trnQ-UUG LSC 2358 0.0085 1.00 70.3 yes View details
trnG-GCC-trnR-UCU LSC 254 0.0209 0.96 57.3 yes View details
rpoB-trnC-GCA LSC 1259 0.0078 1.00 65.4 yes View details
petN-psbM LSC 1157 0.0087 1.00 70.1 yes View details
ndhC-trnV-UAC LSC 1176 0.0078 0.99 68.6 yes View details
rbcL LSC 1428 0.0084 1.00 53.6 yes View details
ycf1 IRb 1059 0.0019 1.00 45.8 no View details
ndhF-rpl32 SSC 953 0.0082 1.00 56.0 yes View details
rpl32-trnL-UAG SSC 853 0.0112 1.00 62.8 yes View details
psaC SSC 246 0.0020 1.00 23.1 yes View details
ycf1 SSC 5685 0.0050 1.00 43.9 yes View details
trnK-UUU-rps16 LSC 734 0.0085 1.00 70.3 yes View details
ndhD-psaC SSC 154 0.0356 0.96 68.1 yes View details
trnT-UGU-trnL-UAA LSC 856 0.0073 1.00 67.7 yes View details
trnS-GCU-trnG-GCC LSC 677 0.0089 0.97 66.2 yes View details
rps2-rpoC2 LSC 221 0.0121 1.00 64.8 yes View details
trnE-UUC-trnT-GGU LSC 858 0.0083 0.99 63.5 yes View details
ycf3-trnS-GGA LSC 544 0.0058 1.00 62.7 yes View details
trnS-UGA-lhbA LSC 354 0.0094 1.00 62.1 yes View details
atpH-atpI LSC 1138 0.0069 1.00 61.6 yes View details
trnC-GCA-petN LSC 882 0.0049 1.00 60.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATGCATGAACGTAACGCTCA 395–528 1.000 88.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGCATGAACGTAACGCTCAT 394–527 1.000 88.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ATGCATGAACGTAACGCTCA 409–542 1.000 88.7
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGCATGAACGTAACGCTCAT 408–541 1.000 88.7
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGCATGAACGTAACGCTCAT 407–540 1.000 88.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 TAGTCTGGACGAATCCCTCC GGTGCTCAACCTACAGGAAC 913–1042 0.990 86.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 856–985 0.990 86.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 855–984 0.990 86.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC GGTGCTCAACCTACAGGAAC 871–1000 0.990 85.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 865–994 0.990 85.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA GAGGTTCGAATCCTTCCGTC 2294–2424 1.000 89.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGGATCGAACATCAATTGC GAGGTTCGAATCCTTCCGTC 2283–2413 1.000 87.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CTTCCTTCTCTTCGGGATCG GAGGTTCGAATCCTTCCGTC 2295–2425 1.000 86.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA TTCGGAGGTTCGAATCCTTC 2298–2428 1.000 84.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCCTTCTCTTCGGGATCGA TAAGGCAACGGGTTTTGGTC 2324–2454 0.990 83.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AATCAAACCGAAAGACCCCT 766–797 1.000 82.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ATCAAACCGAAAGACCCCTT 765–796 1.000 82.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA AATCAAACCGAAAGACCCCT 815–846 1.000 81.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ATCAAACCGAAAGACCCCTT 814–845 1.000 81.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAATCAAACCGAAAGACCCCT 767–798 1.000 81.0
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 297–343 1.000 75.3
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 300–346 1.000 75.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 303–349 1.000 74.7
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 306–352 1.000 74.5
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 301–347 1.000 72.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1209–1234 1.000 83.8
atpH-atpI_p2 atpH-atpI GCCAACTCCAGGTCCAATAG TTTTTGCAACTTTAGCCGCG 1258–1283 1.000 83.4
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTTGCAACTTTAGCCGCG 1225–1250 1.000 82.8
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1210–1235 1.000 82.6
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1224–1249 1.000 82.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (101)

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

Species Accession Length (bp) Link
Ilex aculeolata NC_084028.1 157923 View on NCBI ↗
Ilex angulata NC_083993.1 157687 View on NCBI ↗
Ilex aquifolium PQ351777.1 157573 View on NCBI ↗
Ilex asprella NC_045274.1 157856 View on NCBI ↗
Ilex asprella var. tapuensis MT767004.1 157671 View on NCBI ↗
Ilex bioritsensis NC_088090.1 157574 View on NCBI ↗
Ilex buergeri NC_088091.1 157569 View on NCBI ↗
Ilex cassine NC_088092.1 157828 View on NCBI ↗
Ilex cauliflora NC_084037.1 157565 View on NCBI ↗
Ilex centrochinensis NC_083985.1 157228 View on NCBI ↗
Ilex championii NC_057157.1 157468 View on NCBI ↗
Ilex chapaensis NC_057160.1 157665 View on NCBI ↗
Ilex chengkouensis NC_084029.1 157219 View on NCBI ↗
Ilex chinensis NC_088093.1 157887 View on NCBI ↗
Ilex cinerea NC_057156.1 157215 View on NCBI ↗
Ilex corallina NC_083986.1 157215 View on NCBI ↗
Ilex cornuta NC_044416.1 157224 View on NCBI ↗
Ilex cornuta x Ilex latifolia NC_062459.1 157575 View on NCBI ↗
Ilex crenata MW528027.1 157988 View on NCBI ↗
Ilex cyrtura NC_083987.1 157990 View on NCBI ↗
Ilex dabieshanensis NC_056201.1 157218 View on NCBI ↗
Ilex dasyphylla NC_057161.1 158009 View on NCBI ↗
Ilex decidua NC_084036.1 157736 View on NCBI ↗
Ilex delavayi KX426470.1 157671 View on NCBI ↗
Ilex dicarpa NC_083992.1 157829 View on NCBI ↗
Ilex dimorphophylla NC_083988.1 157575 View on NCBI ↗
Ilex dumosa KP016927.1 157732 View on NCBI ↗
Ilex dunniana PQ351776.1 157215 View on NCBI ↗
Ilex editicostata NC_083989.1 158017 View on NCBI ↗
Ilex ficoidea NC_057153.1 157536 View on NCBI ↗
Ilex forrestii NC_084013.1 157885 View on NCBI ↗
Ilex fragilis NC_083990.1 157849 View on NCBI ↗
Ilex fukienensis NC_068753.1 157474 View on NCBI ↗
Ilex graciliflora NC_057158.1 157119 View on NCBI ↗
Ilex hainanensis NC_083991.1 157860 View on NCBI ↗
Ilex hanceana NC_057155.1 157478 View on NCBI ↗
Ilex hirsuta NC_084040.1 157983 View on NCBI ↗
Ilex hylonoma NC_084014.1 157222 View on NCBI ↗
Ilex hylonoma var. glabra PQ351779.1 157851 View on NCBI ↗
Ilex integra NC_044417.1 157548 View on NCBI ↗
Ilex intermedia NC_056902.1 157577 View on NCBI ↗
Ilex intricata NC_084012.1 157512 View on NCBI ↗
Ilex jingxiensis NC_084038.1 157564 View on NCBI ↗
Ilex kunmingensis NC_084025.1 157550 View on NCBI ↗
Ilex kwangtungensis NC_057151.1 158020 View on NCBI ↗
Ilex lancilimba NC_057982.1 157998 View on NCBI ↗
Ilex latifolia NC_047291.1 157601 View on NCBI ↗
Ilex litseifolia NC_084024.1 157966 View on NCBI ↗
Ilex lohfauensis NC_057150.1 157470 View on NCBI ↗
Ilex macrocarpa NC_069020.1 157798 View on NCBI ↗
Ilex macropoda NC_084023.1 157773 View on NCBI ↗
Ilex memecylifolia NC_057159.1 157842 View on NCBI ↗
Ilex metabaptista NC_069021.1 157841 View on NCBI ↗
Ilex micrococca MN830251.1 157782 View on NCBI ↗
Ilex myrtifolia PQ351787.1 157574 View on NCBI ↗
Ilex nanningensis NC_084030.1 157568 View on NCBI ↗
Ilex nitidissima NC_084042.1 157641 View on NCBI ↗
Ilex nothofagifolia NC_084011.1 157512 View on NCBI ↗
Ilex nuculicava NC_084020.1 157472 View on NCBI ↗
Ilex paraguariensis NC_031207.1 157614 View on NCBI ↗
Ilex pedunculosa NC_069022.1 158007 View on NCBI ↗
Ilex peiradena NC_084032.1 157204 View on NCBI ↗
Ilex pentagona NC_084005.1 157578 View on NCBI ↗
Ilex pernyi NC_058616.1 157220 View on NCBI ↗
Ilex polyneura KX426468.1 157621 View on NCBI ↗
Ilex polypyrena NC_084006.1 157776 View on NCBI ↗
Ilex pubescens NC_057154.1 157872 View on NCBI ↗
Ilex purpurea NC_056900.1 157885 View on NCBI ↗
Ilex qingyuanensis NC_084007.1 157973 View on NCBI ↗
Ilex robustinervosa NC_084039.1 157217 View on NCBI ↗
Ilex rotunda NC_056200.1 157743 View on NCBI ↗
Ilex rubra NC_084035.1 157863 View on NCBI ↗
Ilex rugosa NC_082857.1 157588 View on NCBI ↗
Ilex salicina NC_084008.1 157795 View on NCBI ↗
Ilex serrata NC_084009.1 157739 View on NCBI ↗
Ilex shukunii NC_084017.1 157544 View on NCBI ↗
Ilex sinica NC_084027.1 157816 View on NCBI ↗
Ilex stewardii NC_084031.1 157857 View on NCBI ↗
Ilex suaveolens MN830249.1 157857 View on NCBI ↗
Ilex subrugosa NC_084026.1 157576 View on NCBI ↗
Ilex szechwanensis PQ351773.1 157547 View on NCBI ↗
Ilex tolucana NC_084033.1 157453 View on NCBI ↗
Ilex triflora NC_057152.1 157706 View on NCBI ↗
Ilex tsiangiana NC_084021.1 157978 View on NCBI ↗
Ilex venulosa NC_084041.1 157967 View on NCBI ↗
Ilex venusta NC_068754.1 157860 View on NCBI ↗
Ilex verticillata NC_084034.1 157814 View on NCBI ↗
Ilex viridis NC_057162.1 157661 View on NCBI ↗
Ilex vomitoria NC_056901.1 157328 View on NCBI ↗
Ilex wattii subsp. marlipoensis OP104181.1 157570 View on NCBI ↗
Ilex wenchowensis NC_084015.1 157563 View on NCBI ↗
Ilex wilsonii NC_084016.1 157472 View on NCBI ↗
Ilex wilsonii var. handel-mazzettii OP104180.1 157792 View on NCBI ↗
Ilex wuana NC_084022.1 157806 View on NCBI ↗
Ilex wugongshanensis NC_084018.1 157575 View on NCBI ↗
Ilex x altaclerensis NC_057216.1 157518 View on NCBI ↗
Ilex x attenuata NC_057215.1 157833 View on NCBI ↗
Ilex x koehneana NC_056966.1 157538 View on NCBI ↗
Ilex x wandoensis OK328174.1 157216 View on NCBI ↗
Ilex yunnanensis NC_068755.1 157833 View on NCBI ↗
Ilex zhejiangensis NC_068756.1 157182 View on NCBI ↗