Markers + reference

Juglans

14 species · Juglandaceae · Fagales

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Species 14
Genome length 160–161 kb
Candidate markers 277
Primer pairs 90

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 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 820 0.0110 0.98 50.8 yes View details
atpF LSC 1310 0.0017 1.00 28.7 yes View details
trnM-CAU-psbD LSC 1616 0.0086 1.00 67.7 yes View details
lhbA-trnG-UCC LSC 373 0.0184 0.99 55.0 yes View details
ycf4 LSC 555 0.0018 1.00 30.0 yes View details
psaJ-rpl33 LSC 478 0.0036 1.00 38.5 yes View details
ycf1 IRb 1158 0.0030 1.00 36.4 no View details
ndhA SSC 2194 0.0061 1.00 42.7 yes View details
ycf1 SSC 5676 0.0077 1.00 39.2 yes View details
atpA-atpF LSC 65 0.0806 1.00 63.1 yes View details
ndhC-trnV-UAC LSC 561 0.0091 1.00 60.5 yes View details
trnK-UUU-rps16 LSC 1060 0.0100 0.97 57.2 yes View details
psbE-petL LSC 1322 0.0072 1.00 56.7 yes View details
rpl32-trnL-UAG SSC 727 0.0072 0.97 56.2 yes View details
trnF-GAA-ndhJ LSC 840 0.0063 0.98 55.5 yes View details
psbC-trnS-UGA LSC 248 0.0205 1.00 53.9 yes View details
rps16-trnQ-UUG LSC 1501 0.0070 1.00 53.1 yes View details
petA-psbJ LSC 1107 0.0054 1.00 53.0 yes View details
ycf3-trnS-GGA LSC 923 0.0037 1.00 52.1 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 1201–1240 1.000 81.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TTCAAAGAAGGCGGGAGTTT 1202–1241 1.000 81.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TTTCAAAGAAGGCGGGAGTT 1203–1242 1.000 81.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAGAAGGCGGGAGTTTT 1114–1153 1.000 81.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAGAAGGCGGGAGTTT 1115–1154 1.000 81.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AATGGCGGATGTCAGAATCC GAGGTTCGAATCCTTCCGTC 1611–1697 1.000 81.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGAATCCACAACCGACCAT GAGGTTCGAATCCTTCCGTC 1599–1685 1.000 80.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCCACAACCGACCATATCCT GAGGTTCGAATCCTTCCGTC 1594–1680 1.000 80.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1572–1658 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AATGGCGGATGTCAGAATCC TGGCTAAGTGGTAAGGCAAC 1652–1738 1.000 80.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TGGAACGAATCACACTTTTACC 864–904 1.000 60.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TGGAACGAATCACACTTTTACC 863–903 1.000 60.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GGAACGAATCACACTTTTACCA 863–903 1.000 60.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GGAACGAATCACACTTTTACCA 862–902 1.000 60.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACAAAAGCGGAAAGAGAGGG GGAACGAATCACACTTTTACCA 923–963 1.000 59.6
atpA-atpF_p1 atpA-atpF CATCTGCTCGAGTGGTTACC TCATGTTTGGTTCGGGAAGG 562–593 1.000 81.1
atpA-atpF_p2 atpA-atpF CACCCGCCATTACTTCATCA GGGCTATTGAACAGCTGGAA 557–588 1.000 81.0
atpA-atpF_p3 atpA-atpF CACCCGCCATTACTTCATCA TCATGTTTGGTTCGGGAAGG 694–725 1.000 80.9
atpA-atpF_p4 atpA-atpF GTCGCCTACTTGAAGTACGG TCATGTTTGGTTCGGGAAGG 651–682 1.000 80.6
atpA-atpF_p5 atpA-atpF CCATTGCTCCCCTTTCTTGT TCATGTTTGGTTCGGGAAGG 1198–1229 1.000 80.0
atpF_p1 atpF CACCCGCCATTACTTCATCA ATGGGGAAGGACTGATTGGA 1903–1936 1.000 80.9
atpF_p2 atpF CACCCGCCATTACTTCATCA GGACTGGTTGTAGCCTTAGC 2066–2100 1.000 80.8
atpF_p3 atpF CACCCGCCATTACTTCATCA ATTTCTGCCGCTTCCGTTAT 2252–2286 1.000 80.6
atpF_p4 atpF CACCCGCCATTACTTCATCA GCCAAGCTGTAGAAGGGATC 2167–2201 1.000 80.6
atpF_p5 atpF CCATTGCTCCCCTTTCTTGT ATGGGGAAGGACTGATTGGA 2407–2440 1.000 80.4
trnM-CAU-psbD_p1 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1684–1759 1.000 83.1
trnM-CAU-psbD_p2 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1698–1773 1.000 83.0
trnM-CAU-psbD_p3 trnM-CAU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1687–1762 1.000 83.0
trnM-CAU-psbD_p4 trnM-CAU-psbD TCAGTGGTAGAGTAACGCCA GACCGGACCAACCTACAAAA 1701–1776 1.000 82.8
trnM-CAU-psbD_p5 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG TAGACCGGACCAACCTACAA 1700–1775 1.000 82.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Juglans ailanthifolia NC_046433.1 160353 View on NCBI ↗
Juglans cathayensis NC_033893.1 159730 View on NCBI ↗
Juglans cathayensis var. formosana NC_047415.1 159967 View on NCBI ↗
Juglans cinerea NC_035960.1 160288 View on NCBI ↗
Juglans hindsii NC_035965.1 160406 View on NCBI ↗
Juglans hopeiensis NC_033894.1 159714 View on NCBI ↗
Juglans major NC_035966.1 160276 View on NCBI ↗
Juglans major x Juglans regia NC_050065.1 160324 View on NCBI ↗
Juglans mandshurica NC_033892.1 159729 View on NCBI ↗
Juglans microcarpa NC_046432.1 160065 View on NCBI ↗
Juglans nigra NC_035967.1 160274 View on NCBI ↗
Juglans regia NC_028617.1 160537 View on NCBI ↗
Juglans sigillata NC_031373.1 160350 View on NCBI ↗
Juglans sigillata x Juglans regia NC_087753.1 160367 View on NCBI ↗