Markers + reference

Taxodium

2 species · Cupressaceae · Cupressales

Back to catalogue

Species 2
Genome length 132–133 kb
Candidate markers 244
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 244 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbD-trnE-UUC Genome 1512 0.0020 1.00 59.9 yes View details
trnD-GUC-psbM Genome 1737 0.0023 1.00 59.6 yes View details
petN-trnC-GCA Genome 311 0.0032 1.00 46.6 yes View details
atpI-atpH Genome 655 0.0046 1.00 61.8 yes View details
ycf2 Genome 6783 0.0006 1.00 52.8 yes View details
rps3 Genome 693 0.0029 1.00 60.4 yes View details
clpP-accD Genome 1222 0.0039 0.83 62.5 yes View details
trnV-UAC-ndhC Genome 1347 0.0030 1.00 60.5 yes View details
trnI-CAU-psbA Genome 156 0.0000 1.00 71.1 no View details
psbJ-clpP Genome 807 0.0013 0.95 64.2 yes View details
trnI-CAU-ycf2 Genome 710 0.0000 0.88 60.7 yes View details
ndhF-trnN-GUU Genome 830 0.0012 0.99 60.4 yes View details
rps19-rpl22 Genome 91 0.0111 0.99 59.9 yes View details
rpl32-ndhF Genome 659 0.0015 1.00 59.6 yes View details
cemA Genome 786 0.0013 1.00 59.5 yes View details
ycf1-rps12 Genome 776 0.0013 1.00 59.5 yes View details
ndhK Genome 807 0.0012 1.00 59.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbD-trnE-UUC_p1 psbD-trnE-UUC AAGCAATAGACCGGACCAAC CGTTGCCTCCTTGAAAGAGA 1675 1.000 77.9
psbD-trnE-UUC_p2 psbD-trnE-UUC ACAAAACGGTCTCTGCGTAG CGTTGCCTCCTTGAAAGAGA 1647 1.000 77.0
psbD-trnE-UUC_p3 psbD-trnE-UUC AACAAAACGGTCTCTGCGTA CGTTGCCTCCTTGAAAGAGA 1648 1.000 77.0
psbD-trnE-UUC_p4 psbD-trnE-UUC AAGCAATAGACCGGACCAAC GAAAGAGAGATGTCCTGGGC 1663 1.000 76.7
psbD-trnE-UUC_p5 psbD-trnE-UUC ACAAAACGGTCTCTGCGTAG GAAAGAGAGATGTCCTGGGC 1635 1.000 75.8
trnD-GUC-psbM_p1 trnD-GUC-psbM TTAGAGTACCGCCCTGTCAA GCTTGACTCGCCGTTTTTAC 1890–1891 1.000 79.2
trnD-GUC-psbM_p2 trnD-GUC-psbM ATTGGTTAGAGTACCGCCCT GCTTGACTCGCCGTTTTTAC 1895–1896 1.000 78.7
trnD-GUC-psbM_p3 trnD-GUC-psbM TTAGAGTACCGCCCTGTCAA CTTGACTCGCCGTTTTTACG 1889–1890 1.000 77.9
trnD-GUC-psbM_p4 trnD-GUC-psbM ATTGGTTAGAGTACCGCCCT CTTGACTCGCCGTTTTTACG 1894–1895 1.000 77.5
trnD-GUC-psbM_p5 trnD-GUC-psbM TTAGAGTACCGCCCTGTCAA CTGTACTTCGGCTTGACTCG 1900–1901 1.000 76.5
petN-trnC-GCA_p1 petN-trnC-GCA TAAAGCCCACTTCTACCCCA GCGACATAGCCAAGTGGTAA 470 1.000 79.6
petN-trnC-GCA_p2 petN-trnC-GCA ACTACCATTAGAGCAGCCCA GCGACATAGCCAAGTGGTAA 422 1.000 79.1
petN-trnC-GCA_p3 petN-trnC-GCA TAAAGCCCACTTCTACCCCA AATCCTCGATCCCCAGTTCA 436 1.000 78.8
petN-trnC-GCA_p4 petN-trnC-GCA TAAAGCCCACTTCTACCCCA ATCCTCGATCCCCAGTTCAA 435 1.000 78.8
petN-trnC-GCA_p5 petN-trnC-GCA ACTACCATTAGAGCAGCCCA ATCCTCGATCCCCAGTTCAA 387 1.000 78.3
atpI-atpH_p1 atpI-atpH CGAATCCATGGAGGGTCATC CCTACGGATAATCCAGCAGC 730–733 1.000 78.6
atpI-atpH_p2 atpI-atpH CGAATCCATGGAGGGTCATC GCCTACGGATAATCCAGCAG 731–734 1.000 78.6
atpI-atpH_p3 atpI-atpH CGAATCCATGGAGGGTCATC AACGGAAGCAGCAGAAATCA 707–710 1.000 78.4
atpI-atpH_p4 atpI-atpH CGAATCCATGGAGGGTCATC ACGGAAGCAGCAGAAATCAA 706–709 1.000 78.4
atpI-atpH_p5 atpI-atpH CGAATCCATGGAGGGTCATC GCCAGGTCCAATAGAAGCAA 752–755 1.000 78.2
rpl32-ndhF_p1 rpl32-ndhF TTTTGCTGCGGCCCAATA GGAAGGAAAGGCACAATCCA 793 1.000 62.7
rpl32-ndhF_p2 rpl32-ndhF CTTTTGCTGCGGCCCAATA GGAAGGAAAGGCACAATCCA 794 1.000 62.6
rpl32-ndhF_p3 rpl32-ndhF TTTTGCTGCGGCCCAATA AGGAGCCTAATCCGATTGGT 828 1.000 61.7
rpl32-ndhF_p4 rpl32-ndhF CTTTTGCTGCGGCCCAATA AGGAGCCTAATCCGATTGGT 829 1.000 61.7
rpl32-ndhF_p5 rpl32-ndhF TTTTGCTGCGGCCCAATA GGCGAACACTCTTAGTTGCT 861 1.000 61.6
ndhF-trnN-GUU_p1 ndhF-trnN-GUU ATGAGATGCTTAGGAGGGGG TTCCTCAGTAGCTCAGTGGT 995–1003 1.000 76.2
ndhF-trnN-GUU_p2 ndhF-trnN-GUU GCTTAGGAGGGGGACGTATA TTCCTCAGTAGCTCAGTGGT 988–996 1.000 75.8
ndhF-trnN-GUU_p3 ndhF-trnN-GUU ATGAGATGCTTAGGAGGGGG CCGATTGGTCGTAGGTTCAA 957–965 1.000 75.7
ndhF-trnN-GUU_p4 ndhF-trnN-GUU GCTTAGGAGGGGGACGTATA CCGATTGGTCGTAGGTTCAA 950–958 1.000 75.4
ndhF-trnN-GUU_p5 ndhF-trnN-GUU AGGAGAGGGAATGAGATGCT TTCCTCAGTAGCTCAGTGGT 1005–1013 1.000 74.3

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
Taxodium distichum var. imbricarium MN535012.1 132613 View on NCBI ↗
Taxodium mucronatum NC_045277.1 132037 View on NCBI ↗