Markers + reference

Pinus

4 species · Pinaceae · Pinales

Back to catalogue

Species 4
Genome length 120–120 kb
Candidate markers 229
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 229 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaM-ycf12 Genome 293 0.0000 1.00 19.1 yes View details
atpH-atpI Genome 691 0.0029 1.00 45.7 yes View details
trnE-UUC-clpP Genome 623 0.0024 0.96 48.2 yes View details
rps18 Genome 303 0.0050 1.00 34.3 yes View details
cemA-ycf4 Genome 667 0.0045 1.00 47.8 yes View details
rps4 Genome 606 0.0033 1.00 47.4 yes View details
psaC-ccsA Genome 1158 0.0056 1.00 53.0 yes View details
trnI-CAU-psbA Genome 155 0.0000 1.00 71.2 no View details
psbJ-petA Genome 991 0.0015 1.00 60.0 yes View details
trnV-GAC-rps12 Genome 1382 0.0007 1.00 59.4 yes View details
psbA-trnK-UUU Genome 534 0.0009 0.99 59.0 yes View details
psaM Genome 93 0.0394 0.97 59.0 yes View details
trnI-CAU-trnF-GAA Genome 1714 0.0003 1.00 58.9 yes View details
rps15-psaC Genome 2118 0.0002 1.00 57.7 yes View details
ycf1 Genome 5271 0.0006 1.00 53.2 yes View details
ycf2 Genome 6144 0.0007 1.00 53.0 yes View details
petN-psbM Genome 895 0.0017 1.00 51.3 yes View details
psaM Genome 93 0.0000 1.00 42.2 no 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
psbA-trnK-UUU_p1 psbA-trnK-UUU GGTAGGGATCATCAAGACGC AGAATTGCAAGCACGGTTTG 756–762 1.000 78.3
psbA-trnK-UUU_p2 psbA-trnK-UUU GTAGGGATCATCAAGACGCC AGAATTGCAAGCACGGTTTG 755–761 1.000 78.3
psbA-trnK-UUU_p3 psbA-trnK-UUU GGTAGGGATCATCAAGACGC AGAGCAGATCATCCACTCCA 705–711 1.000 78.1
psbA-trnK-UUU_p4 psbA-trnK-UUU GTAGGGATCATCAAGACGCC AGAGCAGATCATCCACTCCA 704–710 1.000 78.1
psbA-trnK-UUU_p5 psbA-trnK-UUU GTAGGGATCATCAAGACGCC GCAGATCATCCACTCCATCC 701–707 1.000 78.0
psaM_p1 psaM CCAGGCCAAGAAAAGCAGAA ACTCATTGGGGAGGGAATGA 141–144 1.000 79.6
psaM_p2 psaM CCAGGCCAAGAAAAGCAGAA TCAAACTCATTGGGGAGGGA 145–148 1.000 77.6
psaM_p3 psaM CCAGGCCAAGAAAAGCAGA ACTCATTGGGGAGGGAATGA 141–144 1.000 76.6
psaM_p4 psaM CAGGCCAAGAAAAGCAGAAA ACTCATTGGGGAGGGAATGA 140–143 1.000 75.5
psaM_p5 psaM CCAGGCCAAGAAAAGCAGAA CAAACTCATTGGGGAGGGAA 144–147 1.000 74.8
psaM-ycf12_p1 psaM-ycf12 TCCGTAGAAAGATTCGGGGT CTAAAGGGCCCGATACAACC 813–816 1.000 79.7
psaM-ycf12_p2 psaM-ycf12 TCCGTAGAAAGATTCGGGGT AGCTATTCGGCTTCAACCTG 1324–1327 1.000 79.4
psaM-ycf12_p3 psaM-ycf12 TCCGTAGAAAGATTCGGGGT CCGCCACGATCTGATTGTAA 1004–1007 1.000 79.4
psaM-ycf12_p4 psaM-ycf12 TCCGTAGAAAGATTCGGGGT TGAGCTGCGCAATAACTTCT 777–780 1.000 79.3
psaM-ycf12_p5 psaM-ycf12 TCCGTAGAAAGATTCGGGGT TATACCCGCCACGATCTGAT 1009–1012 1.000 79.2
trnG-UCC_p1 trnG-UCC GGTTGGACAAAAGATCGATCC CGAGTGAATCGTGAAATTATGT 947–949 1.000 40.3
trnG-UCC_p2 trnG-UCC GGTTGGACAAAAGATCGATCC CGAGTGAATCGTGAAATTATGTT 947–949 1.000 40.3
trnG-UCC_p3 trnG-UCC GGTTGGACAAAAGATCGATCCA CGAGTGAATCGTGAAATTATGT 947–949 1.000 40.3
trnG-UCC_p4 trnG-UCC TGGTTGGACAAAAGATCGATCC CGAGTGAATCGTGAAATTATGT 948–950 1.000 40.3
trnG-UCC_p5 trnG-UCC GTTGGACAAAAGATCGATCCA CGAGTGAATCGTGAAATTATGT 946–948 1.000 40.3
atpH-atpI_p1 atpH-atpI AATGGAAGCAAGCCCTACAG TCTTTGCAACTCTAGCTGCA 813 1.000 74.9
atpH-atpI_p2 atpH-atpI CAATGGAAGCAAGCCCTACA TCTTTGCAACTCTAGCTGCA 814 1.000 74.7
atpH-atpI_p3 atpH-atpI AATGGAAGCAAGCCCTACAG TAGGTGAATCCATGGAGGGT 786 1.000 74.6
atpH-atpI_p4 atpH-atpI CAATGGAAGCAAGCCCTACA TAGGTGAATCCATGGAGGGT 787 1.000 74.4
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG TCTTTGCAACTCTAGCTGCA 789 1.000 73.9
petN-psbM_p1 petN-psbM CGGTATAACTTGGGCTGCTT GCAAGCAGTGGAAGCAATTG 989–995 1.000 75.8
petN-psbM_p2 petN-psbM GGGGGAGAAGTGGGCTATAA GCAAGCAGTGGAAGCAATTG 930–936 1.000 74.7
petN-psbM_p3 petN-psbM ACTTGGGCTGCTTTAATGGT GCAAGCAGTGGAAGCAATTG 982–988 1.000 73.7
petN-psbM_p4 petN-psbM CACTCGTAGTATGGGGGAGA GCAAGCAGTGGAAGCAATTG 942–948 1.000 73.3
petN-psbM_p5 petN-psbM TCACTCGTAGTATGGGGGAG GCAAGCAGTGGAAGCAATTG 943–949 1.000 73.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Pinus densata MT732337.1 119617 View on NCBI ↗
Pinus tabuliformis NC_028531.1 119646 View on NCBI ↗
Pinus tabuliformis var. henryi NC_062404.1 119634 View on NCBI ↗
Pinus thunbergii NC_001631.1 119707 View on NCBI ↗