Markers + reference

Hamamelis

3 species · Hamamelidaceae · Saxifragales

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Species 3
Genome length 160–160 kb
Candidate markers 272
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1676 0.0016 1.00 47.0 yes View details
psbK-psbI LSC 383 0.0035 1.00 43.9 yes View details
psbC LSC 1422 0.0000 1.00 35.9 yes View details
psbC-trnS-UGA LSC 218 0.0214 1.00 53.6 yes View details
rbcL LSC 1428 0.0014 1.00 47.1 yes View details
rps18 LSC 306 0.0000 1.00 20.0 yes View details
rps18-rpl20 LSC 291 0.0115 1.00 61.8 yes View details
clpP LSC 2051 0.0007 1.00 58.2 yes View details
rpl22 LSC 420 0.0032 1.00 32.3 yes View details
ycf15-trnL-CAA IRb 629 0.0022 0.98 49.7 yes View details
ndhI SSC 582 0.0023 1.00 59.8 yes View details
ndhA SSC 2177 0.0018 1.00 40.6 yes View details
ycf1 SSC 5547 0.0010 1.00 26.7 yes View details
trnL-CAA-ycf15 IRa 629 0.0022 0.98 49.7 yes View details
trnE-UUC-trnT-GGU LSC 890 0.0015 1.00 59.7 yes View details
rpoC1 LSC 2795 0.0005 1.00 56.4 yes View details
ndhD-psaC SSC 187 0.0000 0.73 49.4 yes View details
psbZ-trnG-GCC LSC 625 0.0021 1.00 48.2 yes View details
ycf4-cemA LSC 892 0.0015 1.00 48.2 yes View details
trnK-UUU-rps16 LSC 880 0.0023 1.00 48.0 yes View details
rpoB-trnC-GCA LSC 1146 0.0012 1.00 47.9 yes View details
trnF-GAA-ndhJ LSC 726 0.0009 1.00 47.9 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAAGGCGCTCAACCTACA 1069–1070 1.000 79.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 1008–1009 1.000 78.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 1007–1008 1.000 78.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGAAGGCGGAGGTTTTTACG 1027–1028 1.000 78.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC AAAAAGGCGCTCAACCTACA 1023–1024 1.000 78.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAAATTGAAATGGGGCGTGG 1812–1814 1.000 80.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1754–1756 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAAATTGAAATGGGGCGTGG 1814–1816 1.000 79.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1805–1807 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1756–1758 1.000 78.6
psbK-psbI_p1 psbK-psbI CCAAATTACCCGAGGCCTAC TCTTCACGTCCAGGATTACG 606 1.000 72.5
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 520 1.000 72.4
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 517 1.000 70.4
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 518 1.000 70.4
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 519 1.000 70.4
rpoC1_p1 rpoC1 GAGAGGACCGAATTCACACC TTGCTCGTTCGAGAACTACG 2969 1.000 79.6
rpoC1_p2 rpoC1 GGAGAGGACCGAATTCACAC TTGCTCGTTCGAGAACTACG 2970 1.000 79.6
rpoC1_p3 rpoC1 CCTAGTTGAACCGGAGAGGA TTGCTCGTTCGAGAACTACG 2982 1.000 78.5
rpoC1_p4 rpoC1 GGACCGAATTCACACCGTAT TTGCTCGTTCGAGAACTACG 2965 1.000 77.3
rpoC1_p5 rpoC1 GAGAGGACCGAATTCACACC GCTCGTTCGAGAACTACGAT 2967 1.000 76.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA CCGGATTTGAACTGGGGAAA 1295–1304 1.000 79.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGTCAAGCCCTGATCAATGA AAAAGGATTTGCAGTCCCCC 1277–1286 1.000 77.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC CCGGATTTGAACTGGGGAAA 1305–1314 1.000 76.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CCGGATTTGAACTGGGGAAA 1225–1234 1.000 74.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC AAAAGGATTTGCAGTCCCCC 1287–1296 1.000 74.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 1031–1054 1.000 78.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 996–1019 1.000 78.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 993–1016 1.000 78.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 1028–1051 1.000 77.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 958–981 1.000 77.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Hamamelis japonica NC_084417.1 159839 View on NCBI ↗
Hamamelis mollis NC_037881.1 159731 View on NCBI ↗
Hamamelis x intermedia ON729366.1 159785 View on NCBI ↗