Markers + reference

Picea

12 species · Pinaceae · Pinales

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Species 12
Genome length 123–124 kb
Candidate markers 238
Primer pairs 80

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 10 remaining regions by MarkerSeek score (out of 238 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI Genome 488 0.0113 1.00 42.9 yes View details
psbJ-petA Genome 1046 0.0055 1.00 44.8 yes View details
trnV-UAC-trnH-GUG Genome 2686 0.0047 1.00 54.0 yes View details
ycf12-psbB Genome 681 0.0133 1.00 64.6 yes View details
ycf1 Genome 5334 0.0059 1.00 49.6 yes View details
psaC-ccsA Genome 1936 0.0056 1.00 50.6 yes View details
rps7-trnL-CAA Genome 1587 0.0068 0.98 60.3 yes View details
trnI-CAU-psbA Genome 150 0.0048 1.00 68.0 no View details
psaI-accD Genome 550 0.0064 0.98 60.4 yes View details
trnK-UUU-chlB Genome 793 0.0038 0.99 59.6 yes View details
ycf4-psaI Genome 566 0.0073 1.00 59.3 yes View details
psbD-trnT-GGU Genome 1313 0.0032 1.00 56.6 yes View details
trnR-ACG-trnN-GUU Genome 740 0.0032 0.99 56.3 yes View details
trnV-GAC-rps12 Genome 1551 0.0046 1.00 56.0 yes View details
ycf3-psaA Genome 624 0.0051 0.99 55.8 yes View details
trnT-GGU-psaM Genome 1261 0.0058 0.98 55.4 yes View details
trnI-CAU-trnF-GAA Genome 1836 0.0049 1.00 55.2 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
trnK-UUU-chlB_p1 trnK-UUU-chlB AGTCGCACTTAAAAGCCGAG AGGTAATGCACGCAGCTAAA 669–871 1.000 79.4
trnK-UUU-chlB_p2 trnK-UUU-chlB TAGTCGCACTTAAAAGCCGA AGGTAATGCACGCAGCTAAA 670–872 1.000 78.2
trnK-UUU-chlB_p3 trnK-UUU-chlB TCGCACTTAAAAGCCGAGTA AGGTAATGCACGCAGCTAAA 667–869 1.000 78.2
trnK-UUU-chlB_p4 trnK-UUU-chlB AGTCGCACTTAAAAGCCGAG CACGACGAAAGGGCATTTTG 702–904 1.000 77.7
trnK-UUU-chlB_p5 trnK-UUU-chlB CGCACTTAAAAGCCGAGTAC AGGTAATGCACGCAGCTAAA 666–868 1.000 77.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GTTCGGTCACTATTGCGGAT 701–706 1.000 81.9
psbK-psbI_p2 psbK-psbI TCAAACTTGCCGAAGAGCTT TTCTCTTCTTCATCTGCCGC 1387–1398 1.000 81.7
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTCTTCTTCATCTGCCGC 1148–1159 1.000 81.7
psbK-psbI_p4 psbK-psbI TCAAACTTGCCGAAGAGCTT GTTCGGTCACTATTGCGGAT 940–948 1.000 81.6
psbK-psbI_p5 psbK-psbI GAATCATCCCTTCCAACCCC TTCTCTTCTTCATCTGCCGC 1415–1426 1.000 81.3
psbJ-petA_p1 psbJ-petA GGGAGTAAGAGAAATGGCCG TGTGGGTGGATTTGGTCAAG 1333–1347 1.000 81.5
psbJ-petA_p2 psbJ-petA TGGAAGGATCCCTCTTTGGT TGTGGGTGGATTTGGTCAAG 1306–1320 1.000 81.4
psbJ-petA_p3 psbJ-petA TGGCTTATGATGTGTTCGGG TGTGGGTGGATTTGGTCAAG 1845–1859 1.000 81.2
psbJ-petA_p4 psbJ-petA AATGCAGTTCATCCAGCGAT TGTGGGTGGATTTGGTCAAG 1610–1624 1.000 81.2
psbJ-petA_p5 psbJ-petA CCGGCCGAATGAGTATTTCA TGTGGGTGGATTTGGTCAAG 1820–1834 1.000 81.1
ycf4-psaI_p1 ycf4-psaI CCAGAAAGAGGATACAAGCCC CGGCTTATTACTTCCGGCAA 727 1.000 70.8
ycf4-psaI_p2 ycf4-psaI CCCAGAAAGAGGATACAAGCC CGGCTTATTACTTCCGGCAA 728 1.000 70.8
ycf4-psaI_p3 ycf4-psaI CCAGAAAGAGGATACAAGCCC GTCGGCTTATTACTTCCGGC 729 1.000 67.2
ycf4-psaI_p4 ycf4-psaI CCCAGAAAGAGGATACAAGCC GTCGGCTTATTACTTCCGGC 730 1.000 67.2
ycf4-psaI_p5 ycf4-psaI CCTAGTGAACCCAGAAAGAGG CGGCTTATTACTTCCGGCAA 737 1.000 66.4
psaI-accD_p1 psaI-accD TTGCCGGAAGTAATAAGCCG TTGATCTGATCGTTCCACGT 675–717 1.000 74.5
psaI-accD_p2 psaI-accD TTGCCGGAAGTAATAAGCCG CAGCTTTACAGTCTTCCTCGT 622–664 1.000 72.4
psaI-accD_p3 psaI-accD TTGCCGGAAGTAATAAGCCG TTTGATCTGATCGTTCCACGT 676–718 1.000 72.3
psaI-accD_p4 psaI-accD GCCGGAAGTAATAAGCCGAC TTGATCTGATCGTTCCACGT 673–715 1.000 71.0
psaI-accD_p5 psaI-accD CCGGAAGTAATAAGCCGACT TTGATCTGATCGTTCCACGT 672–714 1.000 70.2
trnV-UAC-trnH-GUG_p1 trnV-UAC-trnH-GUG TGCATGTTGGGTTCTTGGAA TTCACAATCCACTGCCTTGG 2426–2836 1.000 81.7
trnV-UAC-trnH-GUG_p2 trnV-UAC-trnH-GUG GCCCAATGCGATAAAATGCA TTCACAATCCACTGCCTTGG 2442–2852 1.000 80.5
trnV-UAC-trnH-GUG_p3 trnV-UAC-trnH-GUG ATGCATGTTGGGTTCTTGGA TTCACAATCCACTGCCTTGG 2427–2837 1.000 79.9
trnV-UAC-trnH-GUG_p4 trnV-UAC-trnH-GUG GCATGTTGGGTTCTTGGAAC TTCACAATCCACTGCCTTGG 2425–2835 1.000 78.8
trnV-UAC-trnH-GUG_p5 trnV-UAC-trnH-GUG TGCATGTTGGGTTCTTGGAA CACAATCCACTGCCTTGGT 2424–2834 1.000 76.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Picea abies NC_021456.1 124084 View on NCBI ↗
Picea asperata NC_032367.1 124145 View on NCBI ↗
Picea chihuahuana NC_039584.1 123488 View on NCBI ↗
Picea crassifolia NC_032366.1 124126 View on NCBI ↗
Picea engelmannii NC_041067.1 123542 View on NCBI ↗
Picea glauca NC_028594.1 123266 View on NCBI ↗
Picea jezoensis NC_029374.1 124146 View on NCBI ↗
Picea likiangensis PV543637.1 124207 View on NCBI ↗
Picea mariana NC_050064.1 123961 View on NCBI ↗
Picea neoveitchii NC_043913.1 124234 View on NCBI ↗
Picea obovata PV631374.1 124111 View on NCBI ↗
Picea schrenkiana NC_057270.1 124060 View on NCBI ↗