Markers + reference

Taiwania

2 species · Cupressaceae · Cupressales

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Species 2
Genome length 131–132 kb
Candidate markers 247
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 247 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 Genome 1580 0.0006 1.00 58.9 yes View details
atpA Genome 1515 0.0013 1.00 59.5 yes View details
trnF-GAA-ndhD Genome 275 0.0036 1.00 54.6 yes View details
trnI-GAU-rrn16 Genome 1066 0.0011 0.88 62.1 yes View details
ccsA-clpP1 Genome 530 0.0000 1.00 26.2 yes View details
clpP1 Genome 678 0.0029 1.00 60.4 yes View details
clpP1-accD Genome 442 0.0023 1.00 42.7 yes View details
accD Genome 2220 0.0005 1.00 57.4 yes View details
trnI-CAU-psbA Genome 153 0.0000 1.00 71.2 no View details
trnC-GCA-rpoB Genome 775 0.0000 0.97 61.2 yes View details
matK-trnK-UUU Genome 610 0.0033 1.00 60.6 yes View details
rpl16 Genome 1363 0.0007 1.00 59.2 yes View details
ndhJ-chlN Genome 925 0.0000 1.00 58.9 yes View details
petD-petB Genome 223 0.0000 0.93 56.9 yes View details
rpoC1 Genome 2820 0.0000 1.00 56.3 yes View details
rrn5-rrn4.5 Genome 302 0.0033 1.00 54.4 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
trnK-UUU_p1 trnK-UUU AGCAAGCATATTTCAATAAGCA ACTGCGTATTCCACTTCGAC 2507 1.000 40.1
trnK-UUU_p2 trnK-UUU AGCAAGCATATTTCAATAAGCA GCGTATTCCACTTCGACTGT 2504 1.000 40.1
trnK-UUU_p3 trnK-UUU AGCAAGCATATTTCAATAAGCA TGCGTATTCCACTTCGACTG 2505 1.000 40.1
trnK-UUU_p4 trnK-UUU AGCAAGCATATTTCAATAAGCA TTCCTGCCGTTCAATCACAA 2567 1.000 40.1
trnK-UUU_p5 trnK-UUU AGCAAGCATATTTCAATAAGCA ATTCCTGCCGTTCAATCACA 2568 1.000 40.1
matK-trnK-UUU_p1 matK-trnK-UUU TGCGTAAAGATCTTCCCGAA ACTGCGTATTCCACTTCGAC 772 1.000 71.8
matK-trnK-UUU_p2 matK-trnK-UUU TGCGTAAAGATCTTCCCGAA GCGTATTCCACTTCGACTGT 769 1.000 71.8
matK-trnK-UUU_p3 matK-trnK-UUU TTGCGTAAAGATCTTCCCGA ACTGCGTATTCCACTTCGAC 773 1.000 71.8
matK-trnK-UUU_p4 matK-trnK-UUU TTGCGTAAAGATCTTCCCGA GCGTATTCCACTTCGACTGT 770 1.000 71.8
matK-trnK-UUU_p5 matK-trnK-UUU TGCGTAAAGATCTTCCCGAA TGCGTATTCCACTTCGACTG 770 1.000 71.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CGATGTGGTAGAAAGCAACG 1655 1.000 69.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA CGATGTGGTAGAAAGCAACG 1656 1.000 67.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA CGATGTGGTAGAAAGCAACG 1653 1.000 67.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC CGATGTGGTAGAAAGCAACG 1652 1.000 67.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TGTGGTAGAAAGCAACGTGC 1652 1.000 67.0
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AACTGGGGTTCGAGGATTTG AGCCTTGATCGATAAAACGACA 899–919 1.000 63.0
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AACTGGGGTTCGAGGATTTG GCCTTGATCGATAAAACGACA 898–918 1.000 61.9
trnC-GCA-rpoB_p3 trnC-GCA-rpoB TGCCTTACCACTTGGCTATG AGCCTTGATCGATAAAACGACA 871–891 1.000 61.3
trnC-GCA-rpoB_p4 trnC-GCA-rpoB GAACTGGGGTTCGAGGATTT AGCCTTGATCGATAAAACGACA 900–920 1.000 60.7
trnC-GCA-rpoB_p5 trnC-GCA-rpoB TGCCTTACCACTTGGCTATG GCCTTGATCGATAAAACGACA 870–890 1.000 60.2
rpoC1_p1 rpoC1 TGCTCAGTCGAGAACTACGA GGAAGGCTCCCTTGATCTCT 2986–2996 1.000 74.8
rpoC1_p2 rpoC1 TGCTCAGTCGAGAACTACGA CTGGAAGGCTCCCTTGATCT 2988–2998 1.000 72.4
rpoC1_p3 rpoC1 TGCTCAGTCGAGAACTACGA TGGAAGGCTCCCTTGATCTC 2987–2997 1.000 72.4
rpoC1_p4 rpoC1 TTGCTCAGTCGAGAACTACG GGAAGGCTCCCTTGATCTCT 2987–2997 1.000 71.4
rpoC1_p5 rpoC1 TTGCTCAGTCGAGAACTACG CTGGAAGGCTCCCTTGATCT 2989–2999 1.000 69.0
atpA_p1 atpA CGATCGAGCATAATATAAACCTGC AGCTCTTGTATCCTGTTCCA 1689–1695 1.000 40.1
atpA_p2 atpA CGATCGAGCATAATATAAACCTGC AGCTCTTGTATCCTGTTCCAA 1689–1695 1.000 40.1
atpA_p3 atpA CGATCGAGCATAATATAAACCTGC AGCTCTTGTATCCTGTTCCAAA 1689–1695 1.000 40.1
atpA_p4 atpA CGATCGAGCATAATATAAACCTGC CCATTGTGCTTGTAAATGTTGC 1724–1730 1.000 40.1
atpA_p5 atpA CGATCGAGCATAATATAAACCTGC GCTCTTGTATCCTGTTCCAAAC 1688–1694 1.000 40.1

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
Taiwania cryptomerioides PQ821892.1 131543 View on NCBI ↗
Taiwania flousiana NC_021441.1 131413 View on NCBI ↗