Markers + reference

Macadamia

2 species · Proteaceae · Proteales

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Species 2
Genome length 160–160 kb
Candidate markers 275
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 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1090 0.0055 1.00 47.7 yes View details
trnS-GCU-trnG-UCC LSC 970 0.0177 0.99 68.5 yes View details
petN-psbM LSC 1214 0.0058 1.00 62.1 yes View details
trnT-GGU-psbD LSC 1631 0.0043 1.00 61.3 yes View details
psbC-trnS-UGA LSC 211 0.0286 1.00 69.1 yes View details
psaJ-rpl33 LSC 365 0.0055 0.99 44.4 yes View details
ndhF SSC 2220 0.0041 1.00 44.7 yes View details
ndhD SSC 1506 0.0020 1.00 48.6 yes View details
ndhE SSC 303 0.0099 1.00 45.3 yes View details
ndhD-psaC SSC 132 0.0775 0.98 86.7 yes View details
rpl2-trnH-GUG IRa 83 0.0244 0.99 67.7 no View details
trnG-UCC-trnR-UCU LSC 157 0.0196 0.97 64.2 yes View details
petD-rpoA LSC 173 0.0173 1.00 62.5 yes View details
ndhF-rpl32 SSC 1102 0.0046 0.99 62.2 yes View details
rbcL-accD LSC 735 0.0054 1.00 61.9 yes View details
accD-psaI LSC 712 0.0042 1.00 61.5 yes View details
trnT-UGU-trnL-UAA LSC 649 0.0046 1.00 61.3 yes View details
petB-petD LSC 903 0.0044 1.00 61.3 yes View details
ycf4-cemA LSC 895 0.0034 1.00 61.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 AATAAGCAAGCTCGACCCTG TGATTGCGACGACTTGTTGA 2042–2048 1.000 79.1
rps16_p2 rps16 AATAAGCAAGCTCGACCCTG TGCGACGACTTGTTGATTGA 2038–2044 1.000 79.1
rps16_p3 rps16 CAATAAGCAAGCTCGACCCT TGATTGCGACGACTTGTTGA 2043–2049 1.000 79.1
rps16_p4 rps16 CAATAAGCAAGCTCGACCCT TGCGACGACTTGTTGATTGA 2039–2045 1.000 79.1
rps16_p5 rps16 ACTTGTGTTGGATTGGCACT TGCGACGACTTGTTGATTGA 2168–2174 1.000 78.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TCGAGAGGGGAAGGATGAAA 1161–1166 1.000 78.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CATCGAGAGGGGAAGGATGA 1163–1168 1.000 78.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TCATCGAGAGGGGAAGGATG 1164–1169 1.000 78.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCGAGAGGGGAAGGATGAA 1162–1167 1.000 77.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCATCGAGAGGGGAAGGAT 1165–1170 1.000 75.1
trnG-UCC_p1 trnG-UCC CATTGTACAATGTAGCGGGT GGACTAAAGATGTGTATTCAAATCA 811 1.000 40.4
trnG-UCC_p2 trnG-UCC CATTGTACAATGTAGCGGGT GGACTAAAGATGTGTATTCAAATCAA 811 1.000 40.4
trnG-UCC_p3 trnG-UCC CATTGTACAATGTAGCGGGT GGACTAAAGATGTGTATTCAAATC 811 1.000 40.4
trnG-UCC_p4 trnG-UCC CATTGTACAATGTAGCGGGT TGTGTATTCAAATCAATGATACATGT 801 1.000 40.4
trnG-UCC_p5 trnG-UCC CATTGTACAATGTAGCGGGT GGACTAAAGATGTGTATTCAAAT 811 1.000 40.4
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 232–236 1.000 65.7
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 235–239 1.000 65.5
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 238–242 1.000 65.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 241–245 1.000 64.8
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 236–240 1.000 63.3
petN-psbM_p1 petN-psbM CTTTCGCTCGTAGTATGGGG TGCTACTGCACTCTTCGTTC 1329 1.000 78.8
petN-psbM_p2 petN-psbM TTCGCTCGTAGTATGGGGAA TGCTACTGCACTCTTCGTTC 1327 1.000 78.0
petN-psbM_p3 petN-psbM TTTCGCTCGTAGTATGGGGA TGCTACTGCACTCTTCGTTC 1328 1.000 78.0
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTCTTCGTTC 1315 1.000 77.1
petN-psbM_p5 petN-psbM CTTTCGCTCGTAGTATGGGG GCTACTGCACTCTTCGTTCT 1328 1.000 76.5
trnT-GGU-psbD_p1 trnT-GGU-psbD ATAGTGGCTAGCGGCTGATA CCGCAACCAGTCATCCATAA 1812–1816 1.000 79.7
trnT-GGU-psbD_p2 trnT-GGU-psbD TAGTGGCTAGCGGCTGATAT CCGCAACCAGTCATCCATAA 1811–1815 1.000 79.7
trnT-GGU-psbD_p3 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CCGCAACCAGTCATCCATAA 1771–1775 1.000 79.5
trnT-GGU-psbD_p4 trnT-GGU-psbD GCTAGCGGCTGATATTCAGG CCGCAACCAGTCATCCATAA 1806–1810 1.000 78.0
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCTAGCGGCTGATATTCAG CCGCAACCAGTCATCCATAA 1807–1811 1.000 78.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Macadamia integrifolia NC_025288.1 159714 View on NCBI ↗
Macadamia ternifolia NC_036416.1 159669 View on NCBI ↗