Markers + reference

Carpinus

12 species · Betulaceae · Fagales

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Species 12
Genome length 159–160 kb
Candidate markers 242
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 242 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 1656 0.0028 0.98 63.3 yes View details
trnS-GCT-trnR-TCT LSC 2051 0.0098 0.97 70.3 yes View details
trnT-GGT-psbD LSC 1428 0.0870 0.99 89.9 yes View details
ndhC-trnM-CAT LSC 1420 0.0034 1.00 60.3 yes View details
trnN-GTT-rpl32 SSC 4755 0.0034 0.99 48.2 yes View details
trnF-GAA-ndhJ LSC 787 0.0025 1.00 62.5 yes View details
atpH-atpI LSC 1209 0.0034 0.99 61.0 yes View details
trnQ-TTG-psbK LSC 452 0.0074 1.00 59.2 yes View details
rpl32-trnL-TAG SSC 1018 0.0018 0.98 58.4 yes View details
trnT-TGT-trnF-GAA LSC 1790 0.0030 1.00 57.2 yes View details
psbE-petL LSC 1053 0.0023 1.00 56.3 yes View details
ndhA SSC 2291 0.0012 1.00 56.1 yes View details
petA-psbJ LSC 1107 0.0014 1.00 56.0 yes View details
trnH-GTG-psbA LSC 420 0.0046 0.98 55.5 yes View details
rps16-trnQ-TTG LSC 1439 0.0008 0.98 55.5 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 75 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 524–536 1.000 81.6
trnH-GTG-psbA_p2 trnH-GTG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 538–550 1.000 81.5
trnH-GTG-psbA_p3 trnH-GTG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 537–549 1.000 81.5
trnH-GTG-psbA_p4 trnH-GTG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 539–551 1.000 81.5
trnH-GTG-psbA_p5 trnH-GTG-psbA TATTTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 585–597 0.750 70.9
matK-rps16_p1 matK-rps16 CCATGATCATGAGCAAGTGC AGGCGGGAGTTTTTATGGAC 1798–2002 0.917 71.7
matK-rps16_p2 matK-rps16 CCATGATCATGAGCAAGTGC GCGGGAGTTTTTATGGACCT 1796–2000 0.917 71.7
matK-rps16_p3 matK-rps16 CCATGATCATGAGCAAGTGC TCAAAGAAGGCGGGAGTTTT 1805–2009 0.917 69.8
matK-rps16_p4 matK-rps16 CCATGATCATGAGCAAGTGC ACATTTCAAAGAAGGCGGGA 1810–2014 0.833 67.0
matK-rps16_p5 matK-rps16 CCATGATCATGAGCAAGTGC TTCAAAGAAGGCGGGAGTTT 1806–2010 0.833 66.4
rps16-trnQ-TTG_p1 rps16-trnQ-TTG TCCACAACCGACCATATCCT GAGGTTCGAATCCTTCCGTC 554–1534 1.000 82.7
rps16-trnQ-TTG_p2 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 532–1512 1.000 82.6
rps16-trnQ-TTG_p3 rps16-trnQ-TTG TCCACAACCGACCATATCCT GGGTTTTGGTCCCGGTATTC 575–1555 1.000 79.1
rps16-trnQ-TTG_p4 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 553–1533 1.000 79.0
rps16-trnQ-TTG_p5 rps16-trnQ-TTG CCACAACCGACCATATCCTT GAGGTTCGAATCCTTCCGTC 553–1533 1.000 78.1
trnQ-TTG-psbK_p1 trnQ-TTG-psbK ATAGGTATGCTCTGGGACGG CGTAGGCTTCAGGCAATTTG 626–649 1.000 77.2
trnQ-TTG-psbK_p2 trnQ-TTG-psbK GAATACCGGGACCAAAACCC CGTAGGCTTCAGGCAATTTG 590–613 1.000 76.1
trnQ-TTG-psbK_p3 trnQ-TTG-psbK ATAGGTATGCTCTGGGACGG TAGGCTTCAGGCAATTTGGC 624–647 1.000 75.1
trnQ-TTG-psbK_p4 trnQ-TTG-psbK GACCAAAACCCGTTGCCTTA CGTAGGCTTCAGGCAATTTG 581–604 1.000 75.0
trnQ-TTG-psbK_p5 trnQ-TTG-psbK ATAGGTATGCTCTGGGACGG GTAGGCTTCAGGCAATTTGG 625–648 1.000 74.0
trnS-GCT-trnR-TCT_p1 trnS-GCT-trnR-TCT CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 2027–2139 1.000 69.7
trnS-GCT-trnR-TCT_p2 trnS-GCT-trnR-TCT AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 2026–2138 1.000 69.6
trnS-GCT-trnR-TCT_p3 trnS-GCT-trnR-TCT CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 2033–2145 1.000 69.0
trnS-GCT-trnR-TCT_p4 trnS-GCT-trnR-TCT AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 2032–2144 1.000 69.0
trnS-GCT-trnR-TCT_p5 trnS-GCT-trnR-TCT ACAAAAGCGGAAAGAGAGGG AGAAGACCTCTGTCCTATCCA 2087–2199 1.000 68.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1259–1305 1.000 82.2
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1260–1306 1.000 81.0
atpH-atpI_p3 atpH-atpI ATAGAAGCAAGACCGACAGC TTTTGCAACTTTAGCTGCGG 1292–1338 1.000 80.0
atpH-atpI_p4 atpH-atpI CAGCAGTACCTTGACCAACC TTTTGCAACTTTAGCTGCGG 1321–1367 1.000 78.5
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGCGAATCTATGGAGGGTC 1232–1278 1.000 78.1

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
Carpinus fangiana NC_039936.1 159222 View on NCBI ↗
Carpinus fargesiana NC_039937.1 159484 View on NCBI ↗
Carpinus hebestroma NC_038131.1 159231 View on NCBI ↗
Carpinus laxiflora MK425701.1 159255 View on NCBI ↗
Carpinus monbeigiana NC_039997.1 159450 View on NCBI ↗
Carpinus oblongifolia NC_038092.1 159086 View on NCBI ↗
Carpinus polyneura NC_039998.1 159400 View on NCBI ↗
Carpinus purpurinervis NC_038093.1 159145 View on NCBI ↗
Carpinus rupestris NC_039999.1 158888 View on NCBI ↗
Carpinus tibetana NC_052921.1 158762 View on NCBI ↗
Carpinus tschonoskii NC_039938.1 159505 View on NCBI ↗
Carpinus viminea NC_039939.1 158681 View on NCBI ↗