Markers + reference

Laminaria

2 species · Laminariaceae · Laminariales

Back to catalogue

Species 2
Genome length 130–131 kb
Candidate markers 282
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 10 remaining regions by MarkerSeek score (out of 282 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2-F6D16_pgt004 Genome 5812 0.0141 1.00 52.7 yes View details
F6D16_pgt008-dnaK Genome 379 0.0380 0.97 69.7 yes View details
ycf66-rpl19 Genome 1358 0.0163 0.99 68.7 yes View details
ycf34 Genome 285 0.0351 1.00 58.1 yes View details
psaF-ORF2 Genome 367 0.0390 0.98 63.8 yes View details
rpl33-clpC Genome 306 0.0261 1.00 53.5 yes View details
psaC Genome 246 0.0122 1.00 45.9 yes View details
psbA-cbbx Genome 549 0.0255 1.00 59.3 yes View details
F6D16_pgt018-rns Genome 450 0.0356 1.00 68.1 yes View details
F6D16_pgt016-psaC Genome 70 0.1143 1.00 78.2 yes View details
thiG-F6D16_pgt008 Genome 127 0.0496 0.95 76.4 yes View details
F6D16_pgt005-F6D16_pgt006 Genome 47 0.0426 1.00 70.9 yes View details
F6D16_pgt007-ORF1 Genome 62 0.0645 1.00 70.0 yes View details
rps10-psaE Genome 54 0.0741 1.00 69.5 yes View details
ftsH-psbH Genome 101 0.0886 0.78 68.8 yes View details
rpl21-rrn5 Genome 96 0.0220 1.00 68.0 no View details
psaL-rbcR Genome 51 0.0392 1.00 67.5 yes View details
F6D16_pgt002-rrns Genome 118 0.0254 1.00 67.1 yes View details
rns-F6D16_pgt019 Genome 118 0.0254 1.00 67.1 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
F6D16_pgt002-rrns_p1 F6D16_pgt002-rrns GCCATCCTGGATTTGAACCA GACTGGGGTGAAGTCGTAAC 245 1.000 79.2
F6D16_pgt002-rrns_p2 F6D16_pgt002-rrns GCCATCCTGGATTTGAACCA GTAACAAGGTAGCCGTACGG 230 1.000 79.2
F6D16_pgt002-rrns_p3 F6D16_pgt002-rrns AATGGGCCATCCTGGATTTG GACTGGGGTGAAGTCGTAAC 250 1.000 78.7
F6D16_pgt002-rrns_p4 F6D16_pgt002-rrns CAAATGGGCCATCCTGGATT GACTGGGGTGAAGTCGTAAC 252 1.000 78.7
F6D16_pgt002-rrns_p5 F6D16_pgt002-rrns GCCATCCTGGATTTGAACCA AGGTAAGGCTAGTGACTGGG 258 1.000 78.7
rpoC2-F6D16_pgt004_p1 rpoC2-F6D16_pgt004 CCGTTTTTCACCGTTTCGTT AGCATCTAATGTGGGAGAGGA 543 0.500 50.2
rpoC2-F6D16_pgt004_p2 rpoC2-F6D16_pgt004 CCGTTTTTCACCGTTTCGTT AATGTGGGAGAGGAGAAGCC 536 0.500 49.9
rpoC2-F6D16_pgt004_p3 rpoC2-F6D16_pgt004 GCTCCTCTAGAGAAAAGCCG AGCATCTAATGTGGGAGAGGA 854 0.500 49.8
rpoC2-F6D16_pgt004_p4 rpoC2-F6D16_pgt004 GAGCCGTTTTTCACCGTTTC AGCATCTAATGTGGGAGAGGA 546 0.500 49.6
rpoC2-F6D16_pgt004_p5 rpoC2-F6D16_pgt004 GCTCCTCTAGAGAAAAGCCG AATGTGGGAGAGGAGAAGCC 847 0.500 49.6
F6D16_pgt005-F6D16_pgt006_p1 F6D16_pgt005-F6D16_pgt006 CTGCGACTTTCGGGTTATGA CGCAGTTTGGTAGCGTATCT 164 1.000 80.3
F6D16_pgt005-F6D16_pgt006_p2 F6D16_pgt005-F6D16_pgt006 TGCGACTTTCGGGTTATGAG CGCAGTTTGGTAGCGTATCT 163 1.000 80.3
F6D16_pgt005-F6D16_pgt006_p3 F6D16_pgt005-F6D16_pgt006 CTACCAAACTGCTCCACTCC CGCAGTTTGGTAGCGTATCT 134 1.000 79.8
F6D16_pgt005-F6D16_pgt006_p4 F6D16_pgt005-F6D16_pgt006 CTTTCGGGTTATGAGCCCAA CGCAGTTTGGTAGCGTATCT 158 1.000 79.4
F6D16_pgt005-F6D16_pgt006_p5 F6D16_pgt005-F6D16_pgt006 TTTCGGGTTATGAGCCCAAC CGCAGTTTGGTAGCGTATCT 157 1.000 79.0
F6D16_pgt007-ORF1_p1 F6D16_pgt007-ORF1 AAGGGGGCGGATTGTAAATC AGGTCGAGATGGTCCTGATT 198 1.000 80.1
F6D16_pgt007-ORF1_p2 F6D16_pgt007-ORF1 GTCACCTAAAGGAGCATGCA AGGTCGAGATGGTCCTGATT 539 1.000 78.8
F6D16_pgt007-ORF1_p3 F6D16_pgt007-ORF1 TCTTTCCAGCATTGATCGCA AGGTCGAGATGGTCCTGATT 575 1.000 78.7
F6D16_pgt007-ORF1_p4 F6D16_pgt007-ORF1 AATCCGCTGGTTTTCCTACG AGGTCGAGATGGTCCTGATT 182 1.000 78.7
F6D16_pgt007-ORF1_p5 F6D16_pgt007-ORF1 TGTCTCAATTGAAGCACGGT AGGTCGAGATGGTCCTGATT 776 1.000 77.5
thiG-F6D16_pgt008_p1 thiG-F6D16_pgt008 CCAGTTCCAACAATAAGGCG TTTGCGAGTGTAGCTCAGTG 264–270 1.000 74.5
thiG-F6D16_pgt008_p2 thiG-F6D16_pgt008 TCCCAGTTCCAACAATAAGGC TTTGCGAGTGTAGCTCAGTG 266–272 1.000 72.3
thiG-F6D16_pgt008_p3 thiG-F6D16_pgt008 CCCAGTTCCAACAATAAGGC TTTGCGAGTGTAGCTCAGTG 265–271 1.000 71.2
thiG-F6D16_pgt008_p4 thiG-F6D16_pgt008 CCAGTTCCAACAATAAGGCG TGATTTGCGAGTGTAGCTCA 267–273 1.000 70.3
thiG-F6D16_pgt008_p5 thiG-F6D16_pgt008 CCAGTTCCAACAATAAGGCG ATTTGCGAGTGTAGCTCAGT 265–271 1.000 70.2
F6D16_pgt008-dnaK_p1 F6D16_pgt008-dnaK GTTGCGCTCTACCACTGAG CTGCTTCTGCTAACCCAGAA 483–494 1.000 70.2
F6D16_pgt008-dnaK_p2 F6D16_pgt008-dnaK GTTGCGCTCTACCACTGAG ATTGCTGCTTCTGCTAACCC 487–498 1.000 69.7
F6D16_pgt008-dnaK_p3 F6D16_pgt008-dnaK GTTGCGCTCTACCACTGAG TTGCTGCTTCTGCTAACCC 486–497 1.000 65.6
F6D16_pgt008-dnaK_p4 F6D16_pgt008-dnaK CAAGGTTGCGCTCTACCAC CTGCTTCTGCTAACCCAGAA 487–498 1.000 65.5
F6D16_pgt008-dnaK_p5 F6D16_pgt008-dnaK CAAGGTTGCGCTCTACCAC ATTGCTGCTTCTGCTAACCC 491–502 1.000 65.1

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
Laminaria digitata NC_044689.1 130377 View on NCBI ↗
Laminaria rodriguezii NC_057231.1 130541 View on NCBI ↗