Markers + reference

Keteleeria

6 species · Pinaceae · Pinales

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Species 6
Genome length 117–118 kb
Candidate markers 231
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 231 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-ycf12 Genome 512 0.0207 1.00 67.5 yes View details
cemA-ycf4 Genome 897 0.0012 0.99 63.2 yes View details
rbcL-atpB Genome 777 0.0017 1.00 36.4 yes View details
rpl23 Genome 276 0.0031 1.00 42.3 yes View details
ycf3-psaA Genome 655 0.0020 1.00 54.8 yes View details
trnM-CAU-trnG-GCC Genome 158 0.0000 1.00 26.9 yes View details
ycf1 Genome 5661 0.0006 1.00 53.4 yes View details
trnV-GAC-rps12 Genome 1533 0.0007 0.98 48.6 yes View details
trnH-GUG-trnI-CAU Genome 312 0.0011 1.00 26.2 yes View details
trnI-CAU-psbA Genome 146 0.0247 1.00 69.6 no View details
petD Genome 1205 0.0008 1.00 50.1 yes View details
psbD-trnT-GGU Genome 1193 0.0008 1.00 50.1 yes View details
trnS-GGA-ycf3 Genome 762 0.0000 1.00 49.9 yes View details
rpoC2 Genome 3669 0.0005 1.00 48.8 yes View details
rpl32-trnV-GAC Genome 979 0.0016 1.00 47.6 yes View details
cemA Genome 789 0.0008 1.00 46.9 yes View details
psbI-psbB Genome 457 0.0000 0.94 46.9 yes View details
petL-psbE Genome 1174 0.0006 1.00 46.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-ycf12_p1 trnS-GCU-ycf12 TAGTGACCGAACGGAGAGAG TTACCTTTGCGAACTGCTGA 706–801 1.000 79.3
trnS-GCU-ycf12_p2 trnS-GCU-ycf12 CGGAGAGAGAGGGATTCGAA TTACCTTTGCGAACTGCTGA 695–790 1.000 79.0
trnS-GCU-ycf12_p3 trnS-GCU-ycf12 ATAGTGACCGAACGGAGAGA TTACCTTTGCGAACTGCTGA 707–802 1.000 78.1
trnS-GCU-ycf12_p4 trnS-GCU-ycf12 TAGTGACCGAACGGAGAGAG ACCTTTGCGAACTGCTGATA 704–799 1.000 77.5
trnS-GCU-ycf12_p5 trnS-GCU-ycf12 TAGTGACCGAACGGAGAGAG TACCTTTGCGAACTGCTGAT 705–800 1.000 77.5
petL-psbE_p1 petL-psbE AGTAGACGTGGAAGGACTGA GCGTTCTCCTGTATTCCCAG 1246 1.000 75.0
petL-psbE_p2 petL-psbE GACGTGGAAGGACTGAATGA GCGTTCTCCTGTATTCCCAG 1242 1.000 73.7
petL-psbE_p3 petL-psbE AGTAGACGTGGAAGGACTGA GAGCGTTCTCCTGTATTCCC 1248 1.000 73.7
petL-psbE_p4 petL-psbE AGACGTGGAAGGACTGAATG GCGTTCTCCTGTATTCCCAG 1243 1.000 73.6
petL-psbE_p5 petL-psbE GACGTGGAAGGACTGAATGA GAGCGTTCTCCTGTATTCCC 1244 1.000 72.4
cemA_p1 cemA GTAAGTCTCGCACCAAGGAG TTCCTCCTTATGCTCCGTCT 1000 1.000 78.9
cemA_p2 cemA TAAGTCTCGCACCAAGGAGA TTCCTCCTTATGCTCCGTCT 999 1.000 78.2
cemA_p3 cemA GCACCAAGGAGAAGACTGAG TTCCTCCTTATGCTCCGTCT 991 1.000 78.1
cemA_p4 cemA GAAGACTGAGGGGGAGGAAT TTCCTCCTTATGCTCCGTCT 981 1.000 78.0
cemA_p5 cemA GTAAGTCTCGCACCAAGGAG TCCTCCTTATGCTCCGTCTC 999 1.000 77.7
cemA-ycf4_p1 cemA-ycf4 CGGACACTTCCAATTCGTGA TGCGTGTATCCATTGAAGGG 772–1037 1.000 82.3
cemA-ycf4_p2 cemA-ycf4 TCGGACACTTCCAATTCGTG TGCGTGTATCCATTGAAGGG 773–1038 1.000 82.3
cemA-ycf4_p3 cemA-ycf4 CGGACACTTCCAATTCGTGA GCGTGTATCCATTGAAGGGT 771–1036 1.000 82.3
cemA-ycf4_p4 cemA-ycf4 TCGGACACTTCCAATTCGTG GCGTGTATCCATTGAAGGGT 772–1037 1.000 82.3
cemA-ycf4_p5 cemA-ycf4 CGGACACTTCCAATTCGTGA AACAGAAAGCTGCCGAATCA 802–1067 1.000 81.7
rbcL-atpB_p1 rbcL-atpB ACATCCCAACAAAGGACGAC CCCCGAGAACAAGAGGATTG 1321–1323 1.000 79.3
rbcL-atpB_p2 rbcL-atpB ACATCCCAACAAAGGACGAC CCCGAGAACAAGAGGATTGG 1320–1322 1.000 79.3
rbcL-atpB_p3 rbcL-atpB ACATCCCAACAAAGGACGAC TCCAAGAGTAGCTCCACCAA 1611–1613 1.000 79.2
rbcL-atpB_p4 rbcL-atpB ATCTCTCCAGCGCATGAATG TCCAAGAGTAGCTCCACCAA 1743–1745 1.000 79.1
rbcL-atpB_p5 rbcL-atpB CGTAGGGCCTTGAATCCAAA TCCAAGAGTAGCTCCACCAA 1487–1489 1.000 79.1
rpoC2_p1 rpoC2 AGTGACACAAGTATTCCATTGGT CGAAAACAGTCGGATGGTGA 350 1.000 54.7
rpoC2_p2 rpoC2 AGTGACACAAGTATTCCATTGGT TCGAAAACAGTCGGATGGTG 351 1.000 54.7
rpoC2_p3 rpoC2 AGTGACACAAGTATTCCATTGGT ACGATTCGAAAACAGTCGGA 356 1.000 52.9
rpoC2_p4 rpoC2 AGTGACACAAGTATTCCATTGGT TTCGAAAACAGTCGGATGGT 352 1.000 52.0
rpoC2_p5 rpoC2 CCATTGGTTCAAACTTGTCTAGG CGAAAACAGTCGGATGGTGA 335 1.000 51.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Keteleeria davidiana var. calcarea OQ657007.1 117617 View on NCBI ↗
Keteleeria davidiana var. formosana OQ657023.1 117618 View on NCBI ↗
Keteleeria fortunei var. cyclolepis OQ657010.1 117608 View on NCBI ↗
Keteleeria fortunei var. oblonga OQ657016.1 117597 View on NCBI ↗
Keteleeria hainanensis NC_087755.1 117381 View on NCBI ↗
Keteleeria pubescens NC_087754.1 117406 View on NCBI ↗