Markers + reference

Tieghemella

2 species · Sapotaceae · Ericales

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Species 2
Genome length 160–160 kb
Candidate markers 269
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0009 1.00 55.0 yes View details
rps16-trnQ-UUG LSC 2028 0.0030 1.00 59.4 yes View details
rps2 LSC 711 0.0014 1.00 52.4 yes View details
petA LSC 963 0.0000 1.00 40.0 yes View details
petA-psbJ LSC 1088 0.0102 0.99 65.9 yes View details
ndhF-rpl32 SSC 1066 0.0010 0.98 61.5 yes View details
rps15-ycf1 SSC 397 0.0076 1.00 58.9 yes View details
psaA-ycf3 LSC 749 0.0013 1.00 59.5 yes View details
matK-trnK-UUU LSC 736 0.0000 0.99 59.4 yes View details
ycf3-trnS-GGA LSC 865 0.0012 1.00 59.4 yes View details
psbE-petL LSC 1292 0.0008 1.00 59.2 yes View details
rpl20-rps12 LSC 791 0.0000 1.00 59.1 yes View details
trnK-UUU-rps16 LSC 839 0.0000 1.00 59.0 yes View details
trnE-UUC-trnT-GGU LSC 869 0.0000 1.00 58.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GAGCAATAACGCCCTCTTGA AAATTCGTGTGCTTGGGAGT 1197 1.000 79.7
psbA_p2 psbA AAAGGAGCAATAACGCCCTC AAATTCGTGTGCTTGGGAGT 1201 1.000 77.9
psbA_p3 psbA GAGCAATAACGCCCTCTTGA AATTCGTGTGCTTGGGAGTC 1196 1.000 76.1
psbA_p4 psbA AAAGGAGCAATAACGCCCTC AATTCGTGTGCTTGGGAGTC 1200 1.000 74.3
psbA_p5 psbA AGCAATAACGCCCTCTTGAT AAATTCGTGTGCTTGGGAGT 1196 1.000 74.2
matK-trnK-UUU_p1 matK-trnK-UUU ACGAAGTTGTGTTGCTGAGA AACGGTAGAGTACTCGGCTT 811–816 1.000 76.7
matK-trnK-UUU_p2 matK-trnK-UUU ACGAAGTTGTGTTGCTGAGA ACGGTAGAGTACTCGGCTTT 810–815 1.000 76.7
matK-trnK-UUU_p3 matK-trnK-UUU ACGAAGTTGTGTTGCTGAGA GGGTTGCTAACTCAACGGTA 824–829 1.000 74.3
matK-trnK-UUU_p4 matK-trnK-UUU ACGAAGTTGTGTTGCTGAGA TTCGGGTTGCTAACTCAACG 827–832 1.000 74.0
matK-trnK-UUU_p5 matK-trnK-UUU CCATGATCATGAGCAAGTGC ACGGTAGAGTACTCGGCTTT 861–866 1.000 72.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGGCGGAGGTTTTTAAGGA 930–976 1.000 71.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGCGGAGGTTTTTAAGGAA 929–975 1.000 71.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGCGGAGGTTTTTAAGGA 929–975 1.000 71.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGCGGAGGTTTTTAAGGAA 928–974 1.000 71.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC AGGCGGAGGTTTTTAAGGAA 1014–1060 1.000 70.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 2108 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCTGTCTTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 2112 1.000 78.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 2101 1.000 78.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCCTGTCTTT GAGGTTCGAATCCTTCCGTC 2122 1.000 78.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG AAATTTAAATGGGGCGTGGC 2165 1.000 77.0
rps2_p1 rps2 TGAGGTTCACAAATAGTAACCA GCCAATCCACGGTAGAAGAG 900–901 1.000 40.2
rps2_p2 rps2 TGAGGTTCACAAATAGTAACCAA GCCAATCCACGGTAGAAGAG 900–901 1.000 40.2
rps2_p3 rps2 TTGAGGTTCACAAATAGTAACCA GCCAATCCACGGTAGAAGAG 901–902 1.000 40.2
rps2_p4 rps2 GGTTCACAAATAGTAACCAATTCCA GCCAATCCACGGTAGAAGAG 897–898 1.000 40.2
rps2_p5 rps2 TGAGGTTCACAAATAGTAACCA AAAGGGAGGGTAAGTGTGGA 814 1.000 40.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AAGAGAGGTGTCCTGAACCA GAACCGATGACTTACGCCTT 958–959 1.000 79.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCCTCCTTGAAAGAGAGGTG GAACCGATGACTTACGCCTT 968–969 1.000 79.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 1009–1010 1.000 78.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AAGAGAGGTGTCCTGAACCA CCATGGCGTTACTCTACCAC 937–938 1.000 78.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCCTCCTTGAAAGAGAGGTG CCATGGCGTTACTCTACCAC 947–948 1.000 78.7

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
Tieghemella africana MZ274147.1 159778 View on NCBI ↗
Tieghemella heckelii MZ274148.1 159801 View on NCBI ↗