Markers + reference

Corylus

18 species · Betulaceae · Fagales

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Species 18
Genome length 160–160 kb
Candidate markers 270
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCT-trnG-UCC LSC 896 0.0078 0.99 53.6 yes View details
trnG-UCC-trnR-TCT LSC 298 0.0111 0.95 55.4 yes View details
atpH-atpI LSC 1222 0.0044 1.00 57.2 yes View details
accD LSC 1503 0.0023 1.00 30.5 yes View details
trnP-TGG-psaJ LSC 397 0.0086 1.00 42.5 yes View details
ndhF SSC 2241 0.0166 1.00 60.9 yes View details
ndhF-rpl32 SSC 896 0.0067 1.00 48.9 yes View details
rpl32-trnL-TAG SSC 1047 0.0069 0.95 50.3 yes View details
ycf1 SSC 5739 0.0030 1.00 41.5 yes View details
rpoB-trnC-GCA LSC 1263 0.0035 1.00 58.8 yes View details
trnT-GGT-psbD LSC 1407 0.0028 0.99 58.4 yes View details
trnF-GAA-ndhJ LSC 826 0.0038 1.00 56.9 yes View details
rps16-trnQ-TTG LSC 1411 0.0036 1.00 54.3 yes View details
matK-rps16 LSC 1870 0.0031 1.00 51.9 yes View details
trnH-GTG-psbA LSC 428 0.0072 1.00 51.7 yes View details
petN-psbM LSC 954 0.0030 1.00 49.6 yes View details
psbL-psbF LSC 22 0.0214 1.00 49.1 yes View details
trnL-TAG-ccsA SSC 113 0.0141 0.96 48.7 yes View details
ndhA SSC 2290 0.0020 1.00 48.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 538–584 1.000 83.2
trnH-GTG-psbA_p2 trnH-GTG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 552–598 1.000 83.1
trnH-GTG-psbA_p3 trnH-GTG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 551–597 1.000 83.1
trnH-GTG-psbA_p4 trnH-GTG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 553–599 1.000 83.0
trnH-GTG-psbA_p5 trnH-GTG-psbA CGCATGGTGGATTCACAATC GCGCTAACCTTGGTATGGAA 567–613 1.000 80.2
matK-rps16_p1 matK-rps16 TGGGTATAGGAAGTCATGTTGC AGGCGGGAGTTTTTATGGAC 1845–1984 1.000 66.7
matK-rps16_p2 matK-rps16 TGGGTATAGGAAGTCATGTTGC GCGGGAGTTTTTATGGACCT 1843–1982 1.000 66.7
matK-rps16_p3 matK-rps16 TGGGTATAGGAAGTCATGTTGC ACATTTCAAAGAAGGCGGGA 1857–1996 1.000 65.4
matK-rps16_p4 matK-rps16 TGGGTATAGGAAGTCATGTTGC TCAAAGAAGGCGGGAGTTTT 1852–1991 1.000 64.9
matK-rps16_p5 matK-rps16 TGGGTATAGGAAGTCATGTTGC TTCAAAGAAGGCGGGAGTTT 1853–1992 1.000 64.9
rps16-trnQ-TTG_p1 rps16-trnQ-TTG TCCACAACCGACCATATCCT GAGGTTCGAATCCTTCCGTC 1434–1513 1.000 83.3
rps16-trnQ-TTG_p2 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1412–1491 1.000 83.2
rps16-trnQ-TTG_p3 rps16-trnQ-TTG TCCACAACCGACCATATCCT GGGTTTTGGTCCCGGTATTC 1455–1534 1.000 79.6
rps16-trnQ-TTG_p4 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1433–1512 1.000 79.5
rps16-trnQ-TTG_p5 rps16-trnQ-TTG CCACAACCGACCATATCCTT GAGGTTCGAATCCTTCCGTC 1433–1512 1.000 78.6
trnS-GCT-trnG-UCC_p1 trnS-GCT-trnG-UCC CAATCCGACGCTTTAGTCCA GGACCCCTTAACTATTACGGG 957–1008 1.000 71.8
trnS-GCT-trnG-UCC_p2 trnS-GCT-trnG-UCC CAATCCGACGCTTTAGTCCA GGGACCCCTTAACTATTACGG 958–1009 1.000 71.8
trnS-GCT-trnG-UCC_p3 trnS-GCT-trnG-UCC AATCCGACGCTTTAGTCCAC GGACCCCTTAACTATTACGGG 956–1007 1.000 71.8
trnS-GCT-trnG-UCC_p4 trnS-GCT-trnG-UCC AATCCGACGCTTTAGTCCAC GGGACCCCTTAACTATTACGG 957–1008 1.000 71.7
trnS-GCT-trnG-UCC_p5 trnS-GCT-trnG-UCC ACAAAAGCGGAAAGAGAGGG GGACCCCTTAACTATTACGGG 1017–1068 1.000 70.9
trnG-UCC-trnR-TCT_p1 trnG-UCC-trnR-TCT AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 362–388 1.000 70.5
trnG-UCC-trnR-TCT_p2 trnG-UCC-trnR-TCT CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 365–391 1.000 70.3
trnG-UCC-trnR-TCT_p3 trnG-UCC-trnR-TCT AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 368–394 1.000 69.8
trnG-UCC-trnR-TCT_p4 trnG-UCC-trnR-TCT CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 371–397 1.000 69.6
trnG-UCC-trnR-TCT_p5 trnG-UCC-trnR-TCT ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 432–458 1.000 68.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1259–1309 1.000 83.8
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC TTTTGCAACTTTAGCTGCGG 1344–1394 1.000 83.7
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1260–1310 1.000 82.6
atpH-atpI_p4 atpH-atpI CGATCCCTTCTACAGCTTGG TTTTGCAACTTTAGCTGCGG 1345–1395 1.000 82.2
atpH-atpI_p5 atpH-atpI ATAGAAGCAAGACCGACAGC TTTTGCAACTTTAGCTGCGG 1292–1342 1.000 81.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (18)

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

Species Accession Length (bp) Link
Corylus americana NC_045287.1 159912 View on NCBI ↗
Corylus avellana NC_031855.1 159641 View on NCBI ↗
Corylus chinensis NC_032351.1 159915 View on NCBI ↗
Corylus colurna NC_045290.1 159842 View on NCBI ↗
Corylus cornuta NC_045292.1 159857 View on NCBI ↗
Corylus cornuta var. californica MH628459.1 159915 View on NCBI ↗
Corylus fargesii NC_031854.1 159856 View on NCBI ↗
Corylus ferox NC_045288.1 159825 View on NCBI ↗
Corylus ferox var. tibetica NC_039128.1 159894 View on NCBI ↗
Corylus heterophylla NC_031856.1 159587 View on NCBI ↗
Corylus heterophylla var. sutchuenensis MH628447.1 159887 View on NCBI ↗
Corylus jacquemontii NC_045291.1 159862 View on NCBI ↗
Corylus kweichowensis MH628449.1 159879 View on NCBI ↗
Corylus kweichowensis var. brevipes MH628452.1 159822 View on NCBI ↗
Corylus mandshurica NC_039127.1 159833 View on NCBI ↗
Corylus sieboldiana NC_045289.1 159870 View on NCBI ↗
Corylus wangii NC_040995.1 159825 View on NCBI ↗
Corylus yunnanensis NC_039129.1 159769 View on NCBI ↗