Markers + reference

Thuja

3 species · Cupressaceae · Cupressales

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Species 3
Genome length 130–132 kb
Candidate markers 238
Primer pairs 55

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 238 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU Genome 296 0.2000 0.02 63.1 yes View details
trnK-UUU-chlB Genome 2016 0.0988 0.10 62.8 yes View details
clpP-chlN Genome 1530 0.0593 0.96 80.1 yes View details
matK Genome 1518 0.4577 0.04 72.4 yes View details
psbN-psbT Genome 85 0.0247 0.95 72.3 yes View details
atpI-atpH Genome 596 0.0135 0.99 67.7 yes View details
atpE-rbcL Genome 447 0.0098 0.99 66.8 yes View details
chlN-ycf1 Genome 878 0.0285 0.92 66.6 yes View details
rrn5-rrn4.5 Genome 319 0.0334 1.00 66.0 yes View details
trnI-CAU-psbA Genome 150 0.0089 0.95 64.9 no View details
rpl22 Genome 462 0.0245 1.00 63.9 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 55 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU GTGCTAGTGATCCAATCGCA GAAAGCCGTGTGCAATGAAA 487 1.000 82.6
psbA-trnK-UUU_p2 psbA-trnK-UUU GTGCTAGTGATCCAATCGCA CACGGTTTGGGGAGAGATTT 459 1.000 82.1
psbA-trnK-UUU_p3 psbA-trnK-UUU AGTGCTAGTGATCCAATCGC GAAAGCCGTGTGCAATGAAA 488 1.000 81.3
psbA-trnK-UUU_p4 psbA-trnK-UUU ATTCCATAGGCTTGCGCTTT GAAAGCCGTGTGCAATGAAA 461 1.000 81.3
psbA-trnK-UUU_p5 psbA-trnK-UUU AGTGCTAGTGATCCAATCGC CACGGTTTGGGGAGAGATTT 460 1.000 80.7
trnK-UUU_p1 trnK-UUU CCGAATAGTGGGATGCTACC AGGAATCTTGTTGAACGGCT 2994–2996 1.000 77.1
trnK-UUU_p2 trnK-UUU AGTGGGATGCTACCTCTCTT AGGAATCTTGTTGAACGGCT 2988–2990 1.000 76.3
trnK-UUU_p3 trnK-UUU GTGGGATGCTACCTCTCTTG AGGAATCTTGTTGAACGGCT 2987–2989 1.000 75.9
trnK-UUU_p4 trnK-UUU CCGAATAGTGGGATGCTACC TCCCAACATTTCGGGATTGA 2908–2910 1.000 74.6
trnK-UUU_p5 trnK-UUU CCGAATAGTGGGATGCTACC CCCAACATTTCGGGATTGAC 2907–2909 1.000 74.2
matK_p1 matK TGATCCTGGCAATTGCTCAA GAGGTTATCCGGGGGTTTTC 1591 1.000 83.8
matK_p2 matK TTGATCCTGGCAATTGCTCA GAGGTTATCCGGGGGTTTTC 1592 1.000 83.8
matK_p3 matK ATTTGGTTGGATTTCCGGGT GAGGTTATCCGGGGGTTTTC 1636 1.000 82.9
matK_p4 matK TGATCCTGGCAATTGCTCAA GGTTATCCGGGGGTTTTCAA 1589 1.000 82.4
matK_p5 matK TTGATCCTGGCAATTGCTCA GGTTATCCGGGGGTTTTCAA 1590 1.000 82.4
trnK-UUU-chlB_p1 trnK-UUU-chlB AACGACATGCTGCTTTTTCC CTCACATCGAACCATCTGCA 2606 0.333 49.8
trnK-UUU-chlB_p2 trnK-UUU-chlB AACGACATGCTGCTTTTTCC CGAGAAATGGGGATTCGTGT 2742 0.333 49.8
trnK-UUU-chlB_p3 trnK-UUU-chlB TGAGGAACAGAAGCTCGTTC CTCACATCGAACCATCTGCA 2858 0.333 49.7
trnK-UUU-chlB_p4 trnK-UUU-chlB GATCGCTCTCCTGACTCATG TTTGCTCTGGGTATGGAGGA 2868 0.333 49.7
trnK-UUU-chlB_p5 trnK-UUU-chlB AACGACATGCTGCTTTTTCC TTTGCTCTGGGTATGGAGGA 2427 0.333 49.7
atpI-atpH_p1 atpI-atpH CGAATCCATGGAGGGTCATC CCTACGGATAATCCAGCAGC 674–759 1.000 79.5
atpI-atpH_p2 atpI-atpH CGAATCCATGGAGGGTCATC GCCTACGGATAATCCAGCAG 675–760 1.000 79.5
atpI-atpH_p3 atpI-atpH CGAATCCATGGAGGGTCATC AACGGAAGCAGCAGAAATCA 651–736 1.000 79.5
atpI-atpH_p4 atpI-atpH CGAATCCATGGAGGGTCATC ACGGAAGCAGCAGAAATCAA 650–735 1.000 79.5
atpI-atpH_p5 atpI-atpH CGAATCCATGGAGGGTCATC GCCAGGTCCAATAGAAGCAA 696–781 1.000 79.2
rrn5-rrn4.5_p1 rrn5-rrn4.5 CGAGATGGATTGGTGTGGTT CCACCTCAAGATGAGTGCTC 483–657 1.000 81.3
rrn5-rrn4.5_p2 rrn5-rrn4.5 GATTGGTGTGGTTCCCCTAC CCACCTCAAGATGAGTGCTC 476–650 1.000 81.2
rrn5-rrn4.5_p3 rrn5-rrn4.5 CGAGATGGATTGGTGTGGTT AGACGAGCCGTTAGGTGATA 448–622 1.000 81.2
rrn5-rrn4.5_p4 rrn5-rrn4.5 GATTGGTGTGGTTCCCCTAC AGACGAGCCGTTAGGTGATA 441–615 1.000 81.2
rrn5-rrn4.5_p5 rrn5-rrn4.5 AACCACCAAGTTCGAGATGG CCACCTCAAGATGAGTGCTC 495–669 1.000 80.7

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
Thuja koraiensis NC_048527.1 130027 View on NCBI ↗
Thuja occidentalis NC_042177.1 131602 View on NCBI ↗
Thuja sutchuenensis NC_042176.1 130668 View on NCBI ↗