Markers + reference

Callitris

2 species · Cupressaceae · Cupressales

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Species 2
Genome length 121–124 kb
Candidate markers 227
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 227 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaA Genome 2250 0.4908 0.80 77.7 yes View details
rps14 Genome 303 0.4833 0.99 73.5 yes View details
psbC Genome 1422 0.4790 0.85 80.9 yes View details
psbD Genome 1062 0.5232 0.83 80.3 yes View details
psbD-trnD-GUC Genome 1196 0.5027 0.93 83.0 yes View details
trnE-UUC-psaM Genome 441 0.4784 0.68 72.8 yes View details
ndhJ Genome 525 0.5155 0.92 81.2 yes View details
ndhC-chlN Genome 1146 0.5005 0.87 81.5 yes View details
ycf2-ndhB Genome 745 0.1693 0.94 83.6 yes View details
trnfM-CAU-rbcL Genome 577 0.1358 0.92 83.4 yes View details
trnK-UUU-chlB Genome 940 0.0832 0.97 82.8 yes View details
accD Genome 2034 0.1562 0.96 82.0 yes View details
ycf3-psaA Genome 534 0.3153 0.87 81.2 yes View details
chlN Genome 1359 0.4321 0.84 80.9 yes View details
chlL Genome 873 0.4571 0.84 80.6 yes View details
psbJ-trnK-UUU Genome 453 0.0569 0.93 80.2 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
ycf2-ndhB_p1 ycf2-ndhB GTCTTGTACAGGCGGCAATA ATTCTGGTGTGGATGGCAAG 1652 0.500 58.6
ycf2-ndhB_p2 ycf2-ndhB GTCTTGTACAGGCGGCAATA CTGCTTCAGCTTTAGCCACT 2088 0.500 58.4
ycf2-ndhB_p3 ycf2-ndhB GTCTTGTACAGGCGGCAATA TCAGTCTACGTACGGGAACA 1797 0.500 58.4
ycf2-ndhB_p4 ycf2-ndhB GTCTTGTACAGGCGGCAATA TGTTCAGTCTACGTACGGGA 1800 0.500 58.4
ycf2-ndhB_p5 ycf2-ndhB ACAGGCGGCAATATCTTTGT ATTCTGGTGTGGATGGCAAG 1645 0.500 57.7
ycf3-psaA_p1 ycf3-psaA TGAAAGTTCGGGCTGATACG CTTTGCGAGAGACCTCTTCC 1350 0.500 59.9
ycf3-psaA_p2 ycf3-psaA TGAAAGTTCGGGCTGATACG AACGCTGCAAAGATCAATGC 1648 0.500 59.9
ycf3-psaA_p3 ycf3-psaA TGAAAGTTCGGGCTGATACG CCAATTGCGGTGCAGTAAAG 1627 0.500 59.8
ycf3-psaA_p4 ycf3-psaA TGAAAGTTCGGGCTGATACG GTATTTGGTGTCCTGCCCAA 1788 0.500 59.3
ycf3-psaA_p5 ycf3-psaA AGAACAGGCCATTCAACAGG CTTTGCGAGAGACCTCTTCC 890 0.500 59.3
psaA_p1 psaA TCGCTCGAGTTCTGAATTGG CCGGTTGACCAAAATGAGGA 2712 0.500 59.2
psaA_p2 psaA TCGCTCGAGTTCTGAATTGG ACTAAATGTCCCGTCCAAGC 2998 0.500 59.1
psaA_p3 psaA TCGCTCGAGTTCTGAATTGG ACCACCACTGATAAACACCG 2787 0.500 58.5
psaA_p4 psaA TCGCTCGAGTTCTGAATTGG CTCGGGTAAAGGCTTCTACG 2733 0.500 58.3
psaA_p5 psaA CGGTCCATTGAGCACCTATC CCGGTTGACCAAAATGAGGA 2786 0.500 58.2
rps14_p1 rps14 TTGAAACTCTTGCATGGGCT AAGGTTATGAGCCTTGCGAG 775 0.500 59.8
rps14_p2 rps14 TTGAAACTCTTGCATGGGCT GAACCCGTGTCTTCAAGGTT 789 0.500 59.7
rps14_p3 rps14 TTGAAACTCTTGCATGGGCT CAAATGGGGTACATCGAGCA 690 0.500 59.7
rps14_p4 rps14 TTGAAACTCTTGCATGGGCT TTGAACCCGTGTCTTCAAGG 791 0.500 59.7
rps14_p5 rps14 TTGAAACTCTTGCATGGGCT ACATCGAGCAATCCTTTCCC 680 0.500 59.6
psbC_p1 psbC GGCTCTGGTCTTGAAAACCA GAGATTCGTGCAGCAGAAGA 1725 0.500 59.8
psbC_p2 psbC TGGCTCTGGTCTTGAAAACC GAGATTCGTGCAGCAGAAGA 1726 0.500 59.8
psbC_p3 psbC GGCTCTGGTCTTGAAAACCA GTGCTGCTCTTCTATGTGCT 2012 0.500 59.7
psbC_p4 psbC TGGCTCTGGTCTTGAAAACC GTGCTGCTCTTCTATGTGCT 2013 0.500 59.7
psbC_p5 psbC GGCTCTGGTCTTGAAAACCA GTTGGAGTAGTTGGCCTAGC 1779 0.500 59.6
psbD_p1 psbD AGTGTCCACAATTTCCCCAC AGCAGGGAGAAAGAAAAGCT 1613 0.500 52.2
psbD_p2 psbD CCCACGCAAAAGGTTTTGTT AGCAGGGAGAAAGAAAAGCT 2067 0.500 52.1
psbD_p3 psbD GGGTCCAATTAGTGCGTGAT AGCAGGGAGAAAGAAAAGCT 1700 0.500 52.0
psbD_p4 psbD AGTGGTTTCTTGGTCACGAC AGCAGGGAGAAAGAAAAGCT 1382 0.500 51.9
psbD_p5 psbD CAGTGGTTTCTTGGTCACGA AGCAGGGAGAAAGAAAAGCT 1383 0.500 51.8

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
Callitris pyramidalis MW470972.1 123571 View on NCBI ↗
Callitris rhomboidea NC_034940.1 121117 View on NCBI ↗