Markers + reference

Alaria

5 species · Alariaceae · Laminariales

Back to catalogue

Species 5
Genome length 131–131 kb
Candidate markers 349
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 349 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-UGA-psaD Genome 204 0.0490 0.98 70.2 yes View details
secA-ycf54 Genome 247 0.0498 1.00 78.4 yes View details
thiG Genome 819 0.0171 1.00 56.1 yes View details
ilvH-ycf34 Genome 270 0.0395 1.00 73.2 yes View details
psbA-cbbx Genome 765 0.0507 0.97 84.3 yes View details
trnL-UAG-rns Genome 427 0.0403 1.00 77.0 yes View details
petF Genome 294 0.0595 1.00 72.7 yes View details
trnT-UGU-trnV-UAC Genome 307 0.0555 0.98 76.6 yes View details
ycf41 Genome 300 0.0240 1.00 47.9 yes View details
trnQ-UUG-ycf65 Genome 550 0.0553 1.00 78.6 yes View details
trnL-UAA-trnC-GCA Genome 78 0.0628 1.00 80.2 yes View details
psbC-ycf41 Genome 144 0.0797 0.99 77.8 yes View details
petD-atpA Genome 89 0.0693 0.84 77.4 yes View details
trnG-GCC-psbI Genome 123 0.0569 1.00 75.2 yes View details
rpl32-trnL-UAG Genome 101 0.0401 0.97 73.3 yes View details
ilvB-rps4 Genome 79 0.0835 1.00 73.1 yes View details
trnH-GUG-trnT-UGU Genome 81 0.0370 1.00 70.7 yes View details
clpC-trnK-UUU Genome 142 0.0348 0.96 69.6 yes View details
psbK-ccsA Genome 316 0.0278 1.00 68.8 yes View details
psaI-psbJ Genome 105 0.0419 1.00 68.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petD-atpA_p1 petD-atpA AGGAATTGGAGCTTGTTTACCA AAAAGTGCAATAGATGACGT 172–186 1.000 49.0
petD-atpA_p2 petD-atpA AGGAATTGGAGCTTGTTTACCA AAAAAGTGCAATAGATGACGT 173–187 1.000 49.0
petD-atpA_p3 petD-atpA TGGTTAGGAATTGGAGCTTGT AAAAGTGCAATAGATGACGT 177–191 1.000 48.9
petD-atpA_p4 petD-atpA TGGTTAGGAATTGGAGCTTGT AAAAAGTGCAATAGATGACGT 178–192 1.000 48.9
petD-atpA_p5 petD-atpA TGGTTAGGAATTGGAGCTTGTT AAAAGTGCAATAGATGACGT 177–191 1.000 48.9
trnS-UGA-psaD_p1 trnS-UGA-psaD ACGCGTAAACGTTCATCTGA CTCATAACCCGAAAGTCGCA 717–758 1.000 87.5
trnS-UGA-psaD_p2 trnS-UGA-psaD ACGCGTAAACGTTCATCTGA TCATAACCCGAAAGTCGCAG 716–757 1.000 87.5
trnS-UGA-psaD_p3 trnS-UGA-psaD GGGTTGCTGGGAACACTAAA CTCATAACCCGAAAGTCGCA 769–810 0.400 61.8
trnS-UGA-psaD_p4 trnS-UGA-psaD GGGTTGCTGGGAACACTAAA TCATAACCCGAAAGTCGCAG 768–809 0.400 61.8
trnS-UGA-psaD_p5 trnS-UGA-psaD GGGTTGCTGGGAACACTAAA CGCAGTTTGGTAGCGTATCT 913–954 0.400 60.6
secA-ycf54_p1 secA-ycf54 TAACGCGGGTGAAGTTGAAA TTGCGTGAACGAGTACAACA 861–871 1.000 84.7
secA-ycf54_p2 secA-ycf54 TAACGCGGGTGAAGTTGAAA TGCGTGAACGAGTACAACAT 860–870 1.000 84.2
secA-ycf54_p3 secA-ycf54 ACCCATCCATTCTGCATCAC TTGCGTGAACGAGTACAACA 942–952 1.000 84.1
secA-ycf54_p4 secA-ycf54 ACCCATCCATTCTGCATCAC TGCGTGAACGAGTACAACAT 941–951 1.000 83.6
secA-ycf54_p5 secA-ycf54 TAACGCGGGTGAAGTTGAAA TGTTCAAGCGGGTAGACAAG 1278–1288 1.000 83.2
thiG_p1 thiG TGTTGTACTCGTTCACGCAA TTTGCGAGTGTAGCTCAGTG 1342–1355 1.000 81.0
thiG_p2 thiG ATGTTGTACTCGTTCACGCA TTTGCGAGTGTAGCTCAGTG 1343–1356 1.000 80.5
thiG_p3 thiG GGGGCAATAAAGCTTCCCAT TTTGCGAGTGTAGCTCAGTG 1549–1562 0.800 70.9
thiG_p4 thiG CGTGATATCACCTGTTGGGG TTTGCGAGTGTAGCTCAGTG 1566 0.200 45.9
thiG_p5 thiG CGTGATATCACCTGTTGGGG ACGAAGGATGAACCACAAGC 1971 0.200 43.8
trnG-GCC-psbI_p1 trnG-GCC-psbI GTTGCGCTCTACCACTGAG CCATCAAGAAACCCAAACCG 188–198 1.000 70.3
trnG-GCC-psbI_p2 trnG-GCC-psbI CAAGGTTGCGCTCTACCAC CCATCAAGAAACCCAAACCG 192–202 1.000 65.6
trnG-GCC-psbI_p3 trnG-GCC-psbI AAGGTTGCGCTCTACCACT CCATCAAGAAACCCAAACCG 191–201 1.000 64.8
trnG-GCC-psbI_p4 trnG-GCC-psbI CTCTACCACTGAGCTACACTC CCATCAAGAAACCCAAACCG 182–192 1.000 64.2
trnG-GCC-psbI_p5 trnG-GCC-psbI GCGACATCAACCTTGGCAA CCATCAAGAAACCCAAACCG 208–218 1.000 63.5
ilvH-ycf34_p1 ilvH-ycf34 GAGTTCGAAGCTGATACGGG TGCAAATCGTGAGGGTTCAA 701–721 1.000 85.9
ilvH-ycf34_p2 ilvH-ycf34 AGCAGACCCTGGGAAAATTG TGCAAATCGTGAGGGTTCAA 834–854 1.000 85.8
ilvH-ycf34_p3 ilvH-ycf34 CAGCAGACCCTGGGAAAATT TGCAAATCGTGAGGGTTCAA 835–855 1.000 85.8
ilvH-ycf34_p4 ilvH-ycf34 AAGGATGCAGGAGGGTTAGT TGCAAATCGTGAGGGTTCAA 1187–1207 1.000 85.3
ilvH-ycf34_p5 ilvH-ycf34 ATGCAGGAGGGTTAGTACGT TGCAAATCGTGAGGGTTCAA 1183–1203 1.000 84.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Alaria crassifolia NC_058771.1 130514 View on NCBI ↗
Alaria crispa NC_058768.1 130588 View on NCBI ↗
Alaria esculenta NC_058770.1 130591 View on NCBI ↗
Alaria marginata NC_058769.1 130582 View on NCBI ↗
Alaria praelonga NC_058772.1 130514 View on NCBI ↗