Markers + reference

Fucus

2 species · Fucaceae · Fucales

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Species 2
Genome length 125–125 kb
Candidate markers 340
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 340 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbI-trnG(gcc) LSC 138 0.0073 0.99 43.5 yes View details
chlB LSC 1533 0.0026 1.00 52.4 yes View details
tsf LSC 603 0.0033 1.00 49.7 yes View details
atpF LSC 525 0.0057 1.00 60.5 yes View details
ilvH LSC 651 0.0046 1.00 47.2 yes View details
ORF501 LSC 1506 0.0013 1.00 54.3 yes View details
trnT(tgt)-psbC SSC 247 0.0122 1.00 51.6 yes View details
rpl9 SSC 468 0.0064 1.00 52.0 yes View details
rps11 SSC 372 0.0081 1.00 46.6 yes View details
rpl22 SSC 333 0.0030 1.00 40.3 yes View details
rpl2 SSC 828 0.0048 1.00 61.5 yes View details
rpl20-ilvH LSC 76 0.1053 1.00 81.0 yes View details
ORF76-trnY(gta) LSC 34 0.0882 1.00 78.5 yes View details
psaJ LSC 129 0.0391 0.99 75.7 yes View details
ycf46-ccs1 LSC 34 0.0294 1.00 69.4 yes View details
trnP(tgg) LSC 74 0.0270 1.00 68.0 yes View details
ycf3-atpB LSC 122 0.0246 1.00 66.6 yes View details
psbH-ftsH SSC 62 0.0167 0.97 65.1 yes View details
trnH(gtg)-trnT(tgt) SSC 50 0.0200 1.00 64.0 yes View details
rpl36 SSC 114 0.0175 1.00 62.6 yes View details
rps3 SSC 669 0.0060 1.00 62.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbI-trnG(gcc)_p1 psbI-trnG(gcc) TGATCCATCAAGAAATCCAA CTCTACCACTGAGCTACACTC 201 1.000 40.4
psbI-trnG(gcc)_p2 psbI-trnG(gcc) TGATCCATCAAGAAATCCAAA CTCTACCACTGAGCTACACTC 201 1.000 40.4
psbI-trnG(gcc)_p3 psbI-trnG(gcc) TGATCCATCAAGAAATCCAA TCTACCACTGAGCTACACTC 200 1.000 40.4
psbI-trnG(gcc)_p4 psbI-trnG(gcc) TGATCCATCAAGAAATCCAA CTCTACCACTGAGCTACACT 201 1.000 40.4
psbI-trnG(gcc)_p5 psbI-trnG(gcc) TGATCCATCAAGAAATCCAAA TCTACCACTGAGCTACACTC 200 1.000 40.4
ycf46-ccs1_p1 ycf46-ccs1 ACAAAATTGGGCTTCTTCAGG TGCTCAATAAATGAACCAATACT 175 1.000 40.5
ycf46-ccs1_p2 ycf46-ccs1 ACAAAATTGGGCTTCTTCAGG TTTGCTCAATAAATGAACCAA 177 1.000 40.5
ycf46-ccs1_p3 ycf46-ccs1 ACAAAATTGGGCTTCTTCAGG TTGCTCAATAAATGAACCAATACT 176 1.000 40.5
ycf46-ccs1_p4 ycf46-ccs1 ACAAAATTGGGCTTCTTCAGG TTTTGCTCAATAAATGAACCA 178 1.000 40.4
ycf46-ccs1_p5 ycf46-ccs1 ACAAAATTGGGCTTCTTCAGG TTTTGCTCAATAAATGAACCAA 178 1.000 40.4
ORF76-trnY(gta)_p1 ORF76-trnY(gta) TGTTTGGTGGGATAGAGGGA AAGGGGGCGGATTGTAAATC 137 1.000 78.4
ORF76-trnY(gta)_p2 ORF76-trnY(gta) TGTTTGGTGGGATAGAGGGA GCTGGTTTACCTACGTTGGT 116 1.000 77.9
ORF76-trnY(gta)_p3 ORF76-trnY(gta) TGTTTGGTGGGATAGAGGGA AATCCGCTGGTTTACCTACG 121 1.000 76.7
ORF76-trnY(gta)_p4 ORF76-trnY(gta) TGTTTGGTGGGATAGAGGGA GTTCAAATCCAACTCGGCCT 98 1.000 75.9
ORF76-trnY(gta)_p5 ORF76-trnY(gta) TGTTTGGTGGGATAGAGGGA GTTAAAGGGGGCGGATTGTA 141 1.000 75.5
chlB_p1 chlB TGAGTATTTGAATTTGATACTCTCA GCTACGTCCCGTAAGTCATT 1672 1.000 40.2
chlB_p2 chlB TTGAGTATTTGAATTTGATACTCTCA GCTACGTCCCGTAAGTCATT 1673 1.000 40.2
chlB_p3 chlB TGAGTATTTGAATTTGATACTCTCA CTACCAAACTGCGCTACGTC 1684 1.000 40.2
chlB_p4 chlB TGAGTATTTGAATTTGATACTCTCAT GCTACGTCCCGTAAGTCATT 1672 1.000 40.2
chlB_p5 chlB TGAGTATTTGAATTTGATACTCTCA TACCAAACTGCGCTACGTC 1683 1.000 40.2
trnP(tgg)_p1 trnP(tgg) ATGCCGCTAAAGAATCAGCA CAAACTGCTCTACTCCGCAT 267 1.000 80.1
trnP(tgg)_p2 trnP(tgg) TGCCGCTAAAGAATCAGCAT CAAACTGCTCTACTCCGCAT 266 1.000 80.1
trnP(tgg)_p3 trnP(tgg) ATGCCGCTAAAGAATCAGCA AACGAGCTACCAAACTGCTC 277 1.000 78.6
trnP(tgg)_p4 trnP(tgg) TGCCGCTAAAGAATCAGCAT AACGAGCTACCAAACTGCTC 276 1.000 78.6
trnP(tgg)_p5 trnP(tgg) TGCCGCTAAAGAATCAGCAT CAACGAGCTACCAAACTGCT 277 1.000 76.3
tsf_p1 tsf ACCGTTGGTTAGGAGGTACA ATATCATTGGTTGGGGCTGC 1628 1.000 77.8
tsf_p2 tsf ACCGTTGGTTAGGAGGTACA GCTGCAAATTCACCTTCAGG 1613 1.000 77.3
tsf_p3 tsf ACCGTTGGTTAGGAGGTACA GGCTGCAAATTCACCTTCAG 1614 1.000 77.3
tsf_p4 tsf ACCGTTGGTTAGGAGGTACA CACCTGCCCAATTACAACCA 1564 1.000 77.2
tsf_p5 tsf ACCGTTGGTTAGGAGGTACA ACCTGCCCAATTACAACCAA 1563 1.000 77.1

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
Fucus spiralis MG922855.1 125066 View on NCBI ↗
Fucus vesiculosus NC_016735.1 124986 View on NCBI ↗