Markers + reference

Clematoclethra

2 species · Actinidiaceae · Ericales

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Species 2
Genome length 157–157 kb
Candidate markers 263
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnR-UCU LSC 358 0.0029 0.95 53.5 yes View details
rpoB LSC 3213 0.0012 1.00 41.4 yes View details
trnC-GCA-petN LSC 773 0.0052 1.00 53.6 yes View details
rbcL-accD LSC 686 0.0073 1.00 53.9 yes View details
petA-psbJ LSC 966 0.0063 0.99 63.3 yes View details
rps12-psbB LSC 3168 0.0060 1.00 59.1 yes View details
trnN-GUU-ndhF IRb 986 0.0011 0.91 54.9 yes View details
ndhF-rpl32 SSC 969 0.0052 1.00 61.9 yes View details
ycf1-trnN-GUU IRa 447 0.0000 0.82 48.6 yes View details
trnI-CAU-trnH-GUG IRa 476 0.0991 0.95 88.3 no View details
trnT-UGU-trnL-UAA LSC 661 0.0047 0.96 65.1 yes View details
rps19-rpl2 LSC 52 0.0192 1.00 63.6 yes View details
rps16-trnQ-UUG LSC 871 0.0012 0.96 62.9 yes View details
trnR-ACG-trnN-GUU IRb 584 0.0068 1.00 62.4 yes View details
trnN-GUU-trnR-ACG IRa 584 0.0068 1.00 62.4 yes View details
rpl32-trnL-UAG SSC 797 0.0050 1.00 61.6 yes View details
trnK-UUU-rps16 LSC 800 0.0037 1.00 60.9 yes View details
trnE-UUC-trnT-GGU LSC 816 0.0037 1.00 60.9 yes View details
ndhC-trnV-UAC LSC 899 0.0033 1.00 60.8 yes View details
accD-psaI LSC 603 0.0033 1.00 60.7 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 937 1.000 78.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 936 1.000 78.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGGGCGGAGGTTTTTAAGG 886 1.000 78.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGGCGGAGGTTTTTAAGG 885 1.000 78.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGGCGGAGGTTTTTAAGGAA 883 1.000 78.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 993–1019 1.000 81.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 976–1002 1.000 81.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 994–1020 1.000 80.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TAAGGCACCGGGTTTTGATC 965–991 1.000 80.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCACCGGGTTTTGATC 948–974 1.000 80.2
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 421–438 1.000 66.7
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 424–441 1.000 66.4
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 427–444 1.000 66.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 430–447 1.000 65.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 425–442 1.000 64.2
rpoB_p1 rpoB TGGTGCCAGTATAGACCGAA TCATTGATCAGGGCTTGACG 372 1.000 79.3
rpoB_p2 rpoB TGGTGCCAGTATAGACCGAA GGGCTTGACGGAAGAACTTT 362 1.000 76.4
rpoB_p3 rpoB GGTGCCAGTATAGACCGAAA TCATTGATCAGGGCTTGACG 371 1.000 72.6
rpoB_p4 rpoB TGGTGCCAGTATAGACCGAA CATTGATCAGGGCTTGACGG 371 1.000 71.6
rpoB_p5 rpoB TGGTGCCAGTATAGACCGAA ATCAGGGCTTGACGGAAGAA 366 1.000 71.4
trnC-GCA-petN_p1 trnC-GCA-petN TTGTATCCGTTTGGCGACAT AGCCCAAGCGAGACTTACTA 883–884 1.000 78.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTGTATCCGTTTGGCGACA AGCCCAAGCGAGACTTACTA 884–885 1.000 78.2
trnC-GCA-petN_p3 trnC-GCA-petN TTGTATCCGTTTGGCGACAT AGAGTCCACTTCTTCCCCAT 944–945 1.000 76.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTGTATCCGTTTGGCGACA AGAGTCCACTTCTTCCCCAT 945–946 1.000 76.6
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 847–848 1.000 76.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 899 1.000 78.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 896 1.000 78.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 877 1.000 77.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TGGCGTTACTCTACCACTGA 874 1.000 77.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA ACGACTTACGCCTTACCATG 914 1.000 76.6

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
Clematoclethra scandens NC_069196.1 156875 View on NCBI ↗
Clematoclethra scandens subsp. hemsleyi KX345299.1 156731 View on NCBI ↗