Markers + reference

Sargassum

13 species · Sargassaceae · Fucales

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Species 13
Genome length 124–125 kb
Candidate markers 341
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 341 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf34 Genome 285 0.0363 1.00 57.8 yes View details
rbcS-trnE-UUC Genome 293 0.0562 1.00 73.1 yes View details
orf501 Genome 1413 0.0519 0.99 73.7 yes View details
ccsA-trnL-UAG Genome 213 0.0873 0.98 75.6 yes View details
rrn5-ycf19 Genome 559 0.0490 1.00 81.4 yes View details
ilvB Genome 2676 0.0282 1.00 66.3 yes View details
ycf35 Genome 405 0.0339 1.00 59.2 yes View details
rpl9 Genome 468 0.0312 1.00 62.1 yes View details
chlI-trnF-GAA Genome 195 0.0777 1.00 84.8 yes View details
trnD-GUC-trnM-CAU Genome 177 0.0503 0.97 76.3 yes View details
psbX-ycf66 Genome 215 0.0677 1.00 75.5 yes View details
psaD-trnS-UGA Genome 173 0.0755 1.00 75.1 yes View details
trnN-GUU-rpl9 Genome 252 0.0621 0.97 74.5 yes View details
psbI-trnG-GCC Genome 126 0.0868 1.00 74.2 yes View details
trnC-GCA-rbcL Genome 262 0.0496 0.98 74.1 yes View details
ycf47-trnM-CAU Genome 603 0.0431 1.00 73.4 yes View details
ycf54-secA Genome 112 0.0483 1.00 73.2 yes View details
ycf33-ycf39 Genome 268 0.0459 1.00 73.1 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
chlI-trnF-GAA_p1 chlI-trnF-GAA CGCTTACGAAAAGACCCTTT GAACTGGTGACACGAGGATC 335–427 1.000 79.0
chlI-trnF-GAA_p2 chlI-trnF-GAA CGCTTACGAAAAGACCCTTT TCCACTGCTCTACCAACTGA 310–402 1.000 78.9
chlI-trnF-GAA_p3 chlI-trnF-GAA CGCTTACGAAAAGACCCTTT TTTGAACTGGTGACACGAGG 338–430 1.000 78.6
chlI-trnF-GAA_p4 chlI-trnF-GAA TGTTTACGTCATCGCTTACG GAACTGGTGACACGAGGATC 347–439 0.923 75.5
chlI-trnF-GAA_p5 chlI-trnF-GAA TGTTTACGTCATCGCTTACG TCCACTGCTCTACCAACTGA 322–414 0.923 75.4
ycf47-trnM-CAU_p1 ycf47-trnM-CAU GTTTGGGGTCGTAACGGATT AAATTGCATCTGGCTGGGTT 1156–1181 1.000 86.2
ycf47-trnM-CAU_p2 ycf47-trnM-CAU GTTTGGGGTCGTAACGGATT ATGAGTCCGTTGCCTTCAAC 1103–1128 1.000 85.6
ycf47-trnM-CAU_p3 ycf47-trnM-CAU GTTTGGGGTCGTAACGGATT TCGAACCAGCGTTGTTCTAA 1137–1162 1.000 85.1
ycf47-trnM-CAU_p4 ycf47-trnM-CAU GTTTGGGGTCGTAACGGATT TCGTACTTCCTGCACCTTTC 1799–1832 1.000 84.5
ycf47-trnM-CAU_p5 ycf47-trnM-CAU GTTTGGGGTCGTAACGGATT CGTACTTCCTGCACCTTTCT 1798–1831 1.000 84.5
psbX-ycf66_p1 psbX-ycf66 GCTATAACTCGTGTACCTCCA GCCTAGAAGAAAGTTTGCTCC 280–299 1.000 55.4
psbX-ycf66_p2 psbX-ycf66 TGCTATAACTCGTGTACCTCC GCCTAGAAGAAAGTTTGCTCC 281–300 1.000 55.4
psbX-ycf66_p3 psbX-ycf66 TGCTATAACTCGTGTACCTCCA GCCTAGAAGAAAGTTTGCTCC 281–300 1.000 55.1
psbX-ycf66_p4 psbX-ycf66 GCTATAACTCGTGTACCTCCA AGCCTAGAAGAAAGTTTGCTCC 281–300 1.000 53.7
psbX-ycf66_p5 psbX-ycf66 TGCTATAACTCGTGTACCTCC AGCCTAGAAGAAAGTTTGCTCC 282–301 1.000 53.7
trnD-GUC-trnM-CAU_p1 trnD-GUC-trnM-CAU CCGTGACAGGGTGATACTCT CGACCAAGGGCTTATGAGTC 262–270 1.000 87.0
trnD-GUC-trnM-CAU_p2 trnD-GUC-trnM-CAU TAACTTTCGGGATTGACGGG CGACCAAGGGCTTATGAGTC 302–310 1.000 86.9
trnD-GUC-trnM-CAU_p3 trnD-GUC-trnM-CAU TAACTTTCGGGATTGACGGG GGGCTTATGAGTCCCCTACT 295–303 1.000 86.8
trnD-GUC-trnM-CAU_p4 trnD-GUC-trnM-CAU CCGTGACAGGGTGATACTCT GGGCTTATGAGTCCCCTACT 255–263 1.000 86.7
trnD-GUC-trnM-CAU_p5 trnD-GUC-trnM-CAU TAACTTTCGGGATTGACGGG GACTCTGGCTGGACTTGAAC 325–333 1.000 85.1
psbI-trnG-GCC_p1 psbI-trnG-GCC TCCAAGAGGAGTTCCACAGA GTTGTTTTTGCACCAGCTGT 1247–1276 1.000 86.8
psbI-trnG-GCC_p2 psbI-trnG-GCC TCCAAGAGGAGTTCCACAGA AATTCCTTGACCCGACCCTA 1524–1553 1.000 86.2
psbI-trnG-GCC_p3 psbI-trnG-GCC TCCAAGAGGAGTTCCACAGA TTCCTTGACCCGACCCTATT 1522–1551 1.000 86.2
psbI-trnG-GCC_p4 psbI-trnG-GCC TCCAAGAGGAGTTCCACAGA TTGGCAAGGTTACGCTCTAC 891–906 1.000 85.8
psbI-trnG-GCC_p5 psbI-trnG-GCC AGAGGAGTTCCACAGATCGA GTTGTTTTTGCACCAGCTGT 1243–1272 0.923 82.1
ycf54-secA_p1 ycf54-secA CGTGATGAGCCTGTTGAAGA ACCCATCCATTCTGCATCAC 814–820 0.692 72.9
ycf54-secA_p2 ycf54-secA GCTGTTCGAGCTGGTAGAAA ACCCATCCATTCTGCATCAC 1168–1184 0.615 69.7
ycf54-secA_p3 ycf54-secA AAGGCCTACTTAGCAGGACA ACCCATCCATTCTGCATCAC 1100–1166 0.538 69.5
ycf54-secA_p4 ycf54-secA AGGCCTACTTAGCAGGACAA ACCCATCCATTCTGCATCAC 1099–1165 0.538 69.5
ycf54-secA_p5 ycf54-secA AGGCCTACTTAGCAGGACAA ATTAAAGGTGTCCGGGCTTC 1338–1389 0.462 65.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Sargassum confusum NC_066050.1 124368 View on NCBI ↗
Sargassum feldmannii MW784167.1 124258 View on NCBI ↗
Sargassum graminifolium MW784163.1 124563 View on NCBI ↗
Sargassum henslowianum MW784169.1 124450 View on NCBI ↗
Sargassum ilicifolium var. conduplicatum MW767830.1 124414 View on NCBI ↗
Sargassum kjellmanianum OK323194.1 124385 View on NCBI ↗
Sargassum macrocarpum NC_066458.1 124517 View on NCBI ↗
Sargassum mcclurei MW784168.1 124272 View on NCBI ↗
Sargassum muticum MW784166.1 124401 View on NCBI ↗
Sargassum phyllocystum MW784165.1 124392 View on NCBI ↗
Sargassum polycystum NC_064730.1 124493 View on NCBI ↗
Sargassum serratifolium NC_066459.1 124514 View on NCBI ↗
Sargassum thunbergii NC_029134.1 124592 View on NCBI ↗