Markers + reference

Engelhardia

7 species · Juglandaceae · Fagales

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Species 7
Genome length 161–162 kb
Candidate markers 268
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1021 0.0274 0.99 64.3 yes View details
rps16-trnQ-UUG LSC 1450 0.0133 0.96 58.1 yes View details
trnT-GGU-psbD LSC 1583 0.0146 1.00 64.0 yes View details
trnF-GAA-ndhJ LSC 787 0.0208 0.98 55.6 yes View details
ndhC-trnV-UAC LSC 613 0.0190 0.94 54.8 yes View details
petA-psbJ LSC 1432 0.0228 0.85 59.2 yes View details
trnN-GUU-ndhF IRb 1737 0.0132 0.86 47.7 yes View details
ycf1 SSC 5844 0.0083 1.00 36.4 yes View details
accD-psaI LSC 875 0.0135 0.99 61.5 yes View details
trnS-GCU-trnG-UCC LSC 874 0.0099 0.92 57.5 yes View details
psaA-ycf3 LSC 818 0.0062 0.97 55.2 yes View details
trnW-CCA-trnP-UGG LSC 201 0.0204 0.95 52.8 yes View details
rps19-rpl2 IRb 84 0.0102 1.00 52.6 yes View details
rpl14-rpl16 LSC 141 0.0317 1.00 52.1 yes View details
petL-petG LSC 178 0.0112 1.00 51.0 yes View details
ndhF-rpl32 SSC 944 0.0122 0.77 50.7 yes View details
psbZ-trnG-GCC LSC 417 0.0112 1.00 50.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TCAAAGAAGGCGGGAGTTTT 1201–1238 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TTCAAAGAAGGCGGGAGTTT 1202–1239 1.000 81.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TTTCAAAGAAGGCGGGAGTT 1203–1240 1.000 81.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAGAAGGCGGGAGTTTT 1114–1151 1.000 80.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAGAAGGCGGGAGTTT 1115–1152 1.000 80.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AATGGCGGATGTCAGAATCC GAGGTTCGAATCCTTCCGTC 1038–1613 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGAATCCACAACCGACCAT GAGGTTCGAATCCTTCCGTC 1026–1601 1.000 84.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCCACAACCGACCATATCCT GAGGTTCGAATCCTTCCGTC 1021–1596 1.000 84.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 999–1574 1.000 84.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AATGGCGGATGTCAGAATCC TGGCTAAGTGGTAAGGCAAC 1079–1654 1.000 84.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 893–943 1.000 57.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 892–942 1.000 57.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACAAAAGCGGAAAGAGAGGG ACGAATCACACTTTTACCACT 953–1003 1.000 56.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 896–946 1.000 56.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 895–945 1.000 56.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1733–1892 1.000 83.6
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1747–1906 1.000 83.4
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1736–1895 1.000 83.4
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GACCGGACCAACCTACAAAA 1750–1909 1.000 83.3
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGACCGGACCAACCTACAA 1749–1908 1.000 83.0
psbZ-trnG-GCC_p1 psbZ-trnG-GCC AGTCTTTCTGGTGGGTATCCT ATTGAACCCGCATCTTCTCC 455–738 1.000 75.1
psbZ-trnG-GCC_p2 psbZ-trnG-GCC AGTCTTTCTGGTGGGTATCCT GGATAGCGGGAATTGAACCC 466–749 1.000 72.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC AGTCTTTCTGGTGGGTATCCT GGGAATTGAACCCGCATCTT 459–742 1.000 71.3
psbZ-trnG-GCC_p4 psbZ-trnG-GCC AGTCTTTCTGGTGGGTATCC ATTGAACCCGCATCTTCTCC 455–738 1.000 70.6
psbZ-trnG-GCC_p5 psbZ-trnG-GCC GTCTTTCTGGTGGGTATCCT ATTGAACCCGCATCTTCTCC 454–737 1.000 70.6
psaA-ycf3_p1 psaA-ycf3 TACTTCTGATTCCGGCGAAC ATCAAGCCGCTGAGTATTGG 923–951 1.000 80.4
psaA-ycf3_p2 psaA-ycf3 TACTTCTGATTCCGGCGAAC CAGAGGCTTGGTTCGATCAA 938–966 1.000 79.8
psaA-ycf3_p3 psaA-ycf3 TACTTCTGATTCCGGCGAAC AAGATCACAAGGCGTTTCGA 849–877 1.000 79.6
psaA-ycf3_p4 psaA-ycf3 TACTTCTGATTCCGGCGAAC AGATCACAAGGCGTTTCGAA 848–876 1.000 79.6
psaA-ycf3_p5 psaA-ycf3 TACTTCTGATTCCGGCGAAC CGATCAAGCCGCTGAGTATT 925–953 1.000 79.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Engelhardia fenzelii NC_053704.1 161713 View on NCBI ↗
Engelhardia hybrid cultivar OR208251.1 161520 View on NCBI ↗
Engelhardia roxburghiana NC_046434.1 161164 View on NCBI ↗
Engelhardia serrata NC_081984.1 161519 View on NCBI ↗
Engelhardia spicata NC_081985.1 161642 View on NCBI ↗
Engelhardia spicata var. colebrookeana OR099216.1 161461 View on NCBI ↗
Engelhardia unijuga NC_083211.1 161061 View on NCBI ↗