Markers + reference

Saccharina

4 species · Laminariaceae · Laminariales

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Species 4
Genome length 131–131 kb
Candidate markers 344
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 344 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ilvH LSC 603 0.0293 1.00 54.7 yes View details
psaC-psbA LSC 437 0.0687 1.00 66.8 yes View details
psbA-cbbx LSC 754 0.0544 0.97 76.3 yes View details
trnL2-rns IRa 536 0.0370 0.97 68.1 yes View details
trnT-trnV SSC 283 0.1025 1.00 74.0 yes View details
ycf16 SSC 777 0.0242 1.00 52.6 yes View details
psbC SSC 1425 0.0077 1.00 39.7 yes View details
trnQ-ycf65 SSC 532 0.0486 1.00 67.2 yes View details
atpG-atpH LSC 111 0.0841 1.00 75.6 yes View details
ftsH-psbH SSC 92 0.0743 0.95 73.2 yes View details
trnY-LJCPDNA_020 LSC 62 0.0565 1.00 71.0 yes View details
trnL1-trnC LSC 88 0.0568 1.00 68.3 yes View details
rpl20-ilvH LSC 86 0.0659 1.00 66.7 yes View details
trnG1-psbI LSC 151 0.0651 1.00 65.6 yes View details
psaL-rbcR LSC 51 0.0621 1.00 65.6 yes View details
psbY-rpl32 LSC 340 0.0328 0.99 64.3 yes View details
rpl11-trnW SSC 110 0.0409 1.00 63.7 yes View details
clpC-trnK LSC 138 0.0918 1.00 63.6 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
atpG-atpH_p1 atpG-atpH TCAAAATCGAATAGTCCTCCAGT TTCGCCTTCATGGAAGCTTT 260 1.000 54.5
atpG-atpH_p2 atpG-atpH TCAAAATCGAATAGTCCTCCAGT TTTCGCCTTCATGGAAGCTT 261 1.000 54.5
atpG-atpH_p3 atpG-atpH CCATCAAAATCGAATAGTCCTCC TTCGCCTTCATGGAAGCTTT 263 1.000 52.4
atpG-atpH_p4 atpG-atpH CCATCAAAATCGAATAGTCCTCC TTTCGCCTTCATGGAAGCTT 264 1.000 52.4
atpG-atpH_p5 atpG-atpH TCAAAATCGAATAGTCCTCCAGTT TTCGCCTTCATGGAAGCTTT 260 1.000 51.5
trnY-LJCPDNA_020_p1 trnY-LJCPDNA_020 AAGGGGGCGGATTGTAAATC AGGTCGAGATGGTCCTGATT 198 1.000 80.6
trnY-LJCPDNA_020_p2 trnY-LJCPDNA_020 AATCCGCTGGTTTTCCTACG AGGTCGAGATGGTCCTGATT 182 1.000 79.2
trnY-LJCPDNA_020_p3 trnY-LJCPDNA_020 GCTGGTTTTCCTACGTTGGT AGGTCGAGATGGTCCTGATT 177 1.000 78.2
trnY-LJCPDNA_020_p4 trnY-LJCPDNA_020 GTTCAAATCCAACTCGGCCT AGGTCGAGATGGTCCTGATT 159 1.000 78.0
trnY-LJCPDNA_020_p5 trnY-LJCPDNA_020 GTTAAAGGGGGCGGATTGTA AGGTCGAGATGGTCCTGATT 202 1.000 77.7
trnG1-psbI_p1 trnG1-psbI GTTGCGCTCTACCACTGAG ACCCAAACCGAAAAGATTTCG 206–216 1.000 64.1
trnG1-psbI_p2 trnG1-psbI GTTGCGCTCTACCACTGAG CCCAAACCGAAAAGATTTCGA 205–215 1.000 61.9
trnG1-psbI_p3 trnG1-psbI GTTGCGCTCTACCACTGAG AACCCAAACCGAAAAGATTTCG 207–217 1.000 60.9
trnG1-psbI_p4 trnG1-psbI CAAGGTTGCGCTCTACCAC ACCCAAACCGAAAAGATTTCG 210–220 1.000 59.3
trnG1-psbI_p5 trnG1-psbI GTTGCGCTCTACCACTGAG CCCAAACCGAAAAGATTTCGAA 205–215 1.000 59.3
rpl20-ilvH_p1 rpl20-ilvH AGACCCTTCAGCTTTTTCTGT CCTCCTGCATCCTTTTCAACT 173 1.000 62.3
rpl20-ilvH_p2 rpl20-ilvH AGACCCTTCAGCTTTTTCTGT TCCTCCTGCATCCTTTTCAAC 174 1.000 62.3
rpl20-ilvH_p3 rpl20-ilvH AGACCCTTCAGCTTTTTCTGT TCCTCCTGCATCCTTTTCAA 174 1.000 61.7
rpl20-ilvH_p4 rpl20-ilvH AGACCCTTCAGCTTTTTCTGT CCTCCTGCATCCTTTTCAAC 173 1.000 61.4
rpl20-ilvH_p5 rpl20-ilvH AGACCCTTCAGCTTTTTCTGT ATCCTCCTGCATCCTTTTCA 175 1.000 59.8
ilvH_p1 ilvH GAGGTAATGTCGCTCGGAAC TGCAAATCGTGAGGGTTCAA 1593–1607 1.000 80.7
ilvH_p2 ilvH GAGGTAATGTCGCTCGGAAC CCGTTGATGCAAATCGTGAG 1600–1614 1.000 79.6
ilvH_p3 ilvH GAGGTAATGTCGCTCGGAAC CGTTGATGCAAATCGTGAGG 1599–1613 1.000 79.6
ilvH_p4 ilvH GAGGTAATGTCGCTCGGAAC TCCGTTGATGCAAATCGTGA 1601–1615 1.000 79.3
ilvH_p5 ilvH CGCTCGGAACCGTAGAAATA TGCAAATCGTGAGGGTTCAA 1583 0.500 56.0
trnL1-trnC_p1 trnL1-trnC TTAAGTCCGTTGCGTCTACC TAAGGCCGTGGATTGCAAAT 174–175 1.000 80.1
trnL1-trnC_p2 trnL1-trnC TTAAGTCCGTTGCGTCTACC CCAGTTCGAATCTGGGTGTC 145–146 1.000 79.9
trnL1-trnC_p3 trnL1-trnC TTAAGTCCGTTGCGTCTACC CCGTGGATTGCAAATCCTCT 169–170 1.000 79.5
trnL1-trnC_p4 trnL1-trnC TAAGTCCGTTGCGTCTACCA TAAGGCCGTGGATTGCAAAT 173–174 1.000 76.9
trnL1-trnC_p5 trnL1-trnC TAAGTCCGTTGCGTCTACCA CCGTGGATTGCAAATCCTCT 168–169 1.000 76.3

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
Saccharina japonica NC_018523.1 130584 View on NCBI ↗
Saccharina japonica x Saccharina latissima NC_079820.1 130568 View on NCBI ↗
Saccharina longissima NC_071183.1 130569 View on NCBI ↗
Saccharina subsessilis MZ156036.1 130548 View on NCBI ↗