Markers + reference

Macrocystis

2 species · Laminariaceae · Laminariales

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Species 2
Genome length 129–130 kb
Candidate markers 347
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 347 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 3837 0.0031 1.00 43.1 yes View details
chlB LSC 1533 0.0059 1.00 50.7 yes View details
psbX-rpl27 LSC 430 0.0141 0.99 64.2 yes View details
trnE-psaA LSC 234 0.0214 1.00 64.8 yes View details
chlL LSC 885 0.0045 1.00 55.9 yes View details
psbA-cbbX LSC 698 0.0317 1.00 65.8 yes View details
chlI-trnF LSC 115 0.0261 1.00 67.5 yes View details
trnY-ORF1 LSC 43 0.0233 1.00 65.0 yes View details
rns-ycf37 LSC 944 0.0011 0.96 63.2 no View details
psbJ-psbL LSC 67 0.0149 1.00 61.1 yes View details
ycf42 LSC 561 0.0053 1.00 61.0 yes View details
chlN-psaF LSC 135 0.0148 1.00 61.0 yes View details
atpB LSC 1446 0.0035 1.00 60.7 yes View details
trnP-chlB LSC 73 0.0137 1.00 60.4 yes View details
tsf LSC 603 0.0033 1.00 59.9 yes View details
ycf46 LSC 1476 0.0020 1.00 59.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
chlI-trnF_p1 chlI-trnF TGCTTACGTCACCGTCTAAG GAACTGGTGACACGAGGATC 267 1.000 75.9
chlI-trnF_p2 chlI-trnF TGCTTACGTCACCGTCTAAG TCCACTGCTCTACCAACTGA 242 1.000 75.9
chlI-trnF_p3 chlI-trnF TGCTTACGTCACCGTCTAAG TTTGAACTGGTGACACGAGG 270 1.000 75.5
chlI-trnF_p4 chlI-trnF TGCTTACGTCACCGTCTAAG CTGGTGACACGAGGATCTTC 264 1.000 73.6
chlI-trnF_p5 chlI-trnF GCTTACGTCACCGTCTAAGA GAACTGGTGACACGAGGATC 266 1.000 73.6
tsf_p1 tsf GGGTTCTCACAGTTTCTCCA AGGTCAAACGTTAATCACAACA 720 1.000 44.8
tsf_p2 tsf GGGTTCTCACAGTTTCTCCAG AGGTCAAACGTTAATCACAACA 720 1.000 42.4
tsf_p3 tsf AGGGTTCTCACAGTTTCTCC AGGTCAAACGTTAATCACAACA 721 1.000 42.3
tsf_p4 tsf GGGTTCTCACAGTTTCTCCA AAGGTCAAACGTTAATCACAACA 721 1.000 42.2
tsf_p5 tsf GGGTTCTCACAGTTTCTCCA GGTCAAACGTTAATCACAACA 719 1.000 40.9
rpoC2_p1 rpoC2 TCTGTATCATTTGATTGAAGTGA TCGCCCTATAACTCGGTATGA 201 1.000 41.2
rpoC2_p2 rpoC2 TCTGTATCATTTGATTGAAGTGAA TCGCCCTATAACTCGGTATGA 201 1.000 41.2
rpoC2_p3 rpoC2 TTCTGTATCATTTGATTGAAGTGA TCGCCCTATAACTCGGTATGA 202 1.000 41.2
rpoC2_p4 rpoC2 TTCTGTATCATTTGATTGAAGTGAA TCGCCCTATAACTCGGTATGA 202 1.000 41.2
rpoC2_p5 rpoC2 TCTGTATCATTTGATTGAAGTGA CGCCCTATAACTCGGTATGA 200 1.000 41.2
trnP-chlB_p1 trnP-chlB CCAAAGCAGATACGCTACCA CGAAACACCGAAAAGTTTGCT 197 1.000 68.3
trnP-chlB_p2 trnP-chlB CCAAAGCAGATACGCTACCA CGAAACACCGAAAAGTTTGC 197 1.000 68.0
trnP-chlB_p3 trnP-chlB CCCAAAGCAGATACGCTACC CGAAACACCGAAAAGTTTGCT 198 1.000 67.4
trnP-chlB_p4 trnP-chlB CCCAAAGCAGATACGCTACC CGAAACACCGAAAAGTTTGC 198 1.000 67.1
trnP-chlB_p5 trnP-chlB CCAAAGCAGATACGCTACCA ACACCGAAAAGTTTGCTCAAG 193 1.000 66.6
chlB_p1 chlB ACTAGGTTATTTATGTCAAGAAGA AGAGGGTGTTTCTATTGAACACT 1629 1.000 40.4
chlB_p2 chlB ACTAGGTTATTTATGTCAAGAAGA AGGGTGTTTCTATTGAACACTCT 1627 1.000 40.4
chlB_p3 chlB ACTAGGTTATTTATGTCAAGAAGA GAGGGTGTTTCTATTGAACACTC 1628 1.000 40.4
chlB_p4 chlB ACTAGGTTATTTATGTCAAGAAGA AGGGTGTTTCTATTGAACACTC 1627 1.000 40.4
chlB_p5 chlB ACTAGGTTATTTATGTCAAGAAGA GGGTGTTTCTATTGAACACTCT 1626 1.000 40.4
trnY-ORF1_p1 trnY-ORF1 AAGGGGGCGGATTGTAAATC ACTTAGGTCGAGATGGTCCC 183 1.000 78.1
trnY-ORF1_p2 trnY-ORF1 AAGGGGGCGGATTGTAAATC GTCGAGATGGTCCCGATTTT 177 1.000 77.4
trnY-ORF1_p3 trnY-ORF1 AATCCGCTGGTTTTCCTACG ACTTAGGTCGAGATGGTCCC 167 1.000 76.6
trnY-ORF1_p4 trnY-ORF1 AATCCGCTGGTTTTCCTACG GTCGAGATGGTCCCGATTTT 161 1.000 75.9
trnY-ORF1_p5 trnY-ORF1 GCTGGTTTTCCTACGTTGGT ACTTAGGTCGAGATGGTCCC 162 1.000 75.5

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
Macrocystis integrifolia NC_058274.1 129320 View on NCBI ↗
Macrocystis pyrifera NC_065334.1 130201 View on NCBI ↗