Markers + reference

Fagus

11 species · Fagaceae · Fagales

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Species 11
Genome length 158–158 kb
Candidate markers 264
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 2132 0.0050 1.00 60.0 yes View details
trnS-GCU-trnG-GCC LSC 940 0.0059 1.00 55.4 yes View details
trnM-CAU-psbD LSC 1691 0.0074 0.95 56.3 yes View details
trnS-UGA-psbZ LSC 365 0.0032 1.00 39.0 yes View details
rbcL-psaI LSC 2841 0.0034 1.00 56.1 yes View details
ycf1 IRb 1116 0.0009 1.00 35.9 no View details
ndhF-rpl32 SSC 965 0.0063 0.99 50.7 yes View details
ccsA SSC 957 0.0036 1.00 46.8 yes View details
psaC SSC 246 0.0021 1.00 21.0 yes View details
ycf1 SSC 5676 0.0042 1.00 51.3 yes View details
ndhD-psaC SSC 130 0.0668 0.98 73.9 yes View details
atpH-atpI LSC 1123 0.0027 1.00 61.1 yes View details
psbE-petL LSC 1320 0.0029 1.00 56.7 yes View details
atpF LSC 1316 0.0022 1.00 56.0 yes View details
trnH-GUG-psbA LSC 396 0.0095 1.00 54.7 yes View details
matK LSC 1515 0.0035 1.00 53.0 yes View details
rpoB-trnC-GCA LSC 1261 0.0030 1.00 53.0 yes View details
ycf3 LSC 1992 0.0015 1.00 53.0 yes View details
rpl32-trnL-UAG SSC 1172 0.0045 1.00 53.0 yes View details
rpoC1 LSC 2843 0.0020 1.00 52.8 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-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 514–520 1.000 78.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 528–534 1.000 78.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 527–533 1.000 78.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 529–535 1.000 78.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 515–521 1.000 78.0
matK_p1 matK AGTCGATCAACCCCTATGCT AGCCTGTTTTGACCGTATCG 1718 0.909 73.4
matK_p2 matK AGTCGATCAACCCCTATGCT AGAAATCCCCTATCCCTGCT 1667 0.909 71.5
matK_p3 matK AGTCGATCAACCCCTATGCT GCCTGTTTTGACCGTATCGT 1717 0.909 71.1
matK_p4 matK GTCGATCAACCCCTATGCTT AGCCTGTTTTGACCGTATCG 1717 0.909 70.1
matK_p5 matK GTCGATCAACCCCTATGCTT AGAAATCCCCTATCCCTGCT 1666 0.909 68.2
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG GCGGTCTTACAAGCTCTACC GAGGTTCGAATCCTTCCGTC 2263–2280 1.000 81.1
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2184–2201 1.000 80.5
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2183–2200 1.000 80.5
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CGGTCTTACAAGCTCTACCG GAGGTTCGAATCCTTCCGTC 2262–2279 1.000 80.2
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG ATCAGTCGCGGTCTTACAAG GAGGTTCGAATCCTTCCGTC 2270–2287 1.000 79.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1007–1011 1.000 53.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ACAAAAGCGGAAAGAGAGGG ACGAATCACACTTTTACCACT 1068–1072 1.000 52.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1008–1009 0.909 49.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1011–1012 0.909 48.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1010–1011 0.909 48.3
atpF_p1 atpF TGCTCGAATGGTTACCATGA AGTCTATCTATATCTAAGAGGAGA 1414–1426 1.000 41.0
atpF_p2 atpF GCTCGAATGGTTACCATGAGT AGTCTATCTATATCTAAGAGGAGA 1413–1425 1.000 41.0
atpF_p3 atpF CTGCTCGAATGGTTACCATGA AGTCTATCTATATCTAAGAGGAGA 1415–1427 1.000 41.0
atpF_p4 atpF TCTGCTCGAATGGTTACCATG AGTCTATCTATATCTAAGAGGAGA 1416–1428 1.000 41.0
atpF_p5 atpF TGCTCGAATGGTTACCATGAG AGTCTATCTATATCTAAGAGGAGA 1414–1426 1.000 41.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1004–1214 1.000 83.5
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC TTTTGCAACTTTAGCTGCGG 1089–1299 1.000 83.4
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 974–1184 1.000 83.2
atpH-atpI_p4 atpH-atpI GATCCCTTCTACAGCTTGGC CGAATCCATGGAGGGTCATC 1059–1269 1.000 83.1
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1005–1215 1.000 82.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Fagus crenata NC_041252.1 158372 View on NCBI ↗
Fagus engleriana NC_036929.1 158346 View on NCBI ↗
Fagus grandifolia NC_085418.1 158406 View on NCBI ↗
Fagus hayatae NC_085564.1 158310 View on NCBI ↗
Fagus japonica NC_053352.1 158163 View on NCBI ↗
Fagus japonica var. multinervis NC_060731.1 158349 View on NCBI ↗
Fagus lucida NC_061574.1 158300 View on NCBI ↗
Fagus orientalis OR900533.1 158217 View on NCBI ↗
Fagus sylvatica NC_041437.1 158462 View on NCBI ↗
Fagus sylvatica subsp. sylvatica PP190946.1 158462 View on NCBI ↗
Fagus taurica NC_085604.1 158448 View on NCBI ↗