Markers + reference

Brunellia

2 species · Brunelliaceae · Oxalidales

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Species 2
Genome length 158–158 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnR-UCU LSC 352 0.0176 0.97 61.5 yes View details
rpoB-trnC-GCA LSC 1221 0.0060 0.95 56.9 yes View details
trnE-UUC-trnT-GGU LSC 739 0.0146 0.92 71.1 yes View details
trnT-UGU-trnL-UAA LSC 1024 0.0109 0.99 66.2 yes View details
trnF-GAA-ndhJ LSC 745 0.0083 0.98 56.8 yes View details
rbcL-accD LSC 732 0.0137 1.00 67.0 yes View details
petA-psbJ LSC 1069 0.0159 1.00 67.9 yes View details
rps8 LSC 405 0.0025 1.00 42.0 yes View details
rps19 LSC 279 0.0000 1.00 19.2 yes View details
ndhD SSC 1497 0.0040 1.00 46.9 yes View details
ndhA SSC 2195 0.0055 1.00 60.5 yes View details
ycf1 SSC 5721 0.0081 1.00 56.6 yes View details
ndhD-psaC SSC 140 0.0504 0.99 78.9 yes View details
rps8-rpl14 LSC 220 0.0376 0.97 74.1 yes View details
rps19-rpl2 IRb 70 0.0286 1.00 68.9 yes View details
rpl2-trnH-GUG LSC 243 0.0269 0.92 68.5 no View details
rpl20-rps12 LSC 819 0.0064 0.95 67.0 yes View details
trnK-UUU-rps16 LSC 1312 0.0086 0.88 66.5 yes View details
infA-rps8 LSC 127 0.0394 1.00 65.4 yes View details
rpl22-rps19 LSC 136 0.0737 0.70 65.0 yes View details
trnL-UAG-ccsA SSC 86 0.0123 0.94 64.1 yes View details
ycf3-trnS-GGA LSC 892 0.0067 1.00 63.0 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1322–1439 1.000 81.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1321–1438 1.000 81.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TAAGGCGGGGGTTTTTACAG 1284–1401 1.000 81.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TAAGGCGGGGGTTTTTACAG 1283–1400 1.000 81.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 1331–1448 1.000 80.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 430–435 1.000 66.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 436–441 1.000 65.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 431–436 1.000 64.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGGTTTAGAAGACCTCTGTCCT 437–442 1.000 63.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCAT 430–435 1.000 62.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CGGACTTGAACTGGGGAAAA 1244–1303 1.000 76.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CGGACTTGAACTGGGGAAAA 1249–1308 1.000 75.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CGGACTTGAACTGGGGAAAA 1243–1302 1.000 74.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACATTCCCTCATTTCCATCCC CGGACTTGAACTGGGGAAAA 1251–1310 1.000 73.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC AAAAGGATTTGCAGTCCCCC 1227–1286 1.000 73.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 786–842 1.000 82.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 765–821 1.000 82.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 765–821 1.000 82.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 744–800 1.000 82.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 762–818 1.000 82.2
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA CCCTCGGTAAACAAAAGCCT 1052–1055 1.000 67.3
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA CCCTCGGTAAACAAAAGCCT 1053–1056 1.000 67.3
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 1073–1076 1.000 66.8
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA ACGGAAAGAGAGGGATTCGA 1074–1077 1.000 66.8
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA TGGGTGAAGGTACGGAAAGA 1084–1087 1.000 65.7
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA CAAATGCGAGGCTCTAACCT ACCAATTTCGCCATATCCCC 1078–1093 1.000 81.5
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA CAAATGCGAGGCTCTAACCT TAGCGTCTACCAATTTCGCC 1086–1101 1.000 81.0
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCATTACAAATGCGAGGCTC ACCAATTTCGCCATATCCCC 1084–1099 1.000 80.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCATTACAAATGCGAGGCTC TAGCGTCTACCAATTTCGCC 1092–1107 1.000 80.3
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1105–1120 1.000 79.8

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
Brunellia mexicana NC_069065.1 158142 View on NCBI ↗
Brunellia trianae MN585217.1 157775 View on NCBI ↗