Markers + reference

Gracilariopsis

3 species · Gracilariaceae · Gracilariales

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Species 3
Genome length 182–185 kb
Candidate markers 466
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 466 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn5-rps6 Genome 640 0.1872 0.70 75.1 yes View details
gltB-psaC Genome 532 0.2130 1.00 83.1 yes View details
ycf91 Genome 258 0.1279 1.00 72.5 yes View details
trnR(ccg)-orf441 Genome 806 0.1177 0.96 83.6 yes View details
orf445 Genome 1338 0.1512 1.00 78.8 yes View details
preA-rpl20 Genome 386 0.2038 1.00 79.0 yes View details
acpP Genome 264 0.2096 1.00 72.5 yes View details
petF Genome 297 0.2245 1.00 73.7 yes View details
ompR-rns Genome 1938 0.2960 1.00 84.2 no View details
rns-trnI(gat) Genome 103 0.1295 1.00 82.9 yes View details
orf461-trnM Genome 582 0.0756 1.00 82.9 yes View details
ycf23 Genome 801 0.1082 1.00 82.3 yes View details
psbD-ompR Genome 523 0.1260 0.97 81.8 yes View details
trnN(gtt)-trnL(tag) Genome 155 0.2108 1.00 80.5 yes View details
thiG Genome 831 0.0715 1.00 80.3 yes View details
trnG(tcc)-trnM Genome 55 0.1273 1.00 80.3 yes View details
ycf38 Genome 897 0.0721 1.00 80.1 yes View details
rpl11-trnW(cca) Genome 250 0.1626 0.99 79.8 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
rns-trnI(gat)_p1 rns-trnI(gat) GGGGTGAAGTCGTAACAAGG GGTGGGCTATCCTGGATTTG 227–236 1.000 88.3
rns-trnI(gat)_p2 rns-trnI(gat) CAAGGTAGCCGTACTGGAAG GGTGGGCTATCCTGGATTTG 212–221 1.000 88.2
rns-trnI(gat)_p3 rns-trnI(gat) GGGGTGAAGTCGTAACAAGG GGATTTGAACCAGGGACCTC 214–223 1.000 87.9
rns-trnI(gat)_p4 rns-trnI(gat) AGTAACTGGGGTGAAGTCGT GGTGGGCTATCCTGGATTTG 234–243 1.000 87.3
rns-trnI(gat)_p5 rns-trnI(gat) GGGGTGAAGTCGTAACAAGG ATGGTGGGCTATCCTGGATT 229–238 1.000 87.0
rrn5-rps6_p1 rrn5-rps6 ATCTCCCCCAAGAGTTCACA GACCGCCCATTCATAAGGTT 1841 0.333 52.6
rrn5-rps6_p2 rrn5-rps6 TCTCCCCCAAGAGTTCACAT GACCGCCCATTCATAAGGTT 1840 0.333 52.6
rrn5-rps6_p3 rrn5-rps6 CAAGTCGAGCAGAGACGAAA GACCGCCCATTCATAAGGTT 1941 0.333 52.5
rrn5-rps6_p4 rrn5-rps6 TTCGGTCCATATCCGGTGTA GACCGCCCATTCATAAGGTT 1696 0.333 52.3
rrn5-rps6_p5 rrn5-rps6 CCTTAGTGATCCGACAGTGC GACCGCCCATTCATAAGGTT 1916 0.333 52.3
thiG_p1 thiG AAGCACGAAAAGTTGCTCCT AACGAACAGCAGGAAAAGGA 1854–1858 0.667 63.6
thiG_p2 thiG AACCTTATGAATGGGCGGTC AACGAACAGCAGGAAAAGGA 1793 0.333 50.2
thiG_p3 thiG TATGAATGGGCGGTCAGGTA AACGAACAGCAGGAAAAGGA 1788 0.333 49.0
thiG_p4 thiG TGAATGGGCGGTCAGGTATA AACGAACAGCAGGAAAAGGA 1786 0.333 49.0
thiG_p5 thiG AACCTTATGAATGGGCGGTC ACGAACAGCAGGAAAAGGAT 1792 0.333 48.4
trnN(gtt)-trnL(tag)_p1 trnN(gtt)-trnL(tag) CTCTGCCACTGAGCTACTGA AGCGTGTCTACCAATTCCAC 205–208 1.000 83.0
trnN(gtt)-trnL(tag)_p2 trnN(gtt)-trnL(tag) TCTGCCACTGAGCTACTGAG AGCGTGTCTACCAATTCCAC 204–207 1.000 83.0
trnN(gtt)-trnL(tag)_p3 trnN(gtt)-trnL(tag) CTCTGCCACTGAGCTACTGA TACCAATTCCACCATGTCCG 197–200 1.000 80.6
trnN(gtt)-trnL(tag)_p4 trnN(gtt)-trnL(tag) TCTGCCACTGAGCTACTGAG TACCAATTCCACCATGTCCG 196–199 1.000 80.6
trnN(gtt)-trnL(tag)_p5 trnN(gtt)-trnL(tag) ACCAATCGGTTAACAGCCG AGCGTGTCTACCAATTCCAC 228–231 1.000 80.1
gltB-psaC_p1 gltB-psaC GGGAGGGATTGTCGTTGTTT GTTTCACAGCGCTTACAACC 1036 0.333 52.3
gltB-psaC_p2 gltB-psaC ACGGATAGAACTGTTGGTGC GTTTCACAGCGCTTACAACC 1428 0.333 52.3
gltB-psaC_p3 gltB-psaC TGGTGCTAGGATATCGGGTT GTTTCACAGCGCTTACAACC 1414 0.333 52.3
gltB-psaC_p4 gltB-psaC TTGGTGCTAGGATATCGGGT GTTTCACAGCGCTTACAACC 1415 0.333 52.3
gltB-psaC_p5 gltB-psaC GGGAGGGATTGTCGTTGTTT TTTCACAGCGCTTACAACCT 1035 0.333 52.3
ycf23_p1 ycf23 GGTTGTAAGCGCTGTGAAAC GCTGAGAAATTCTTGTAGCAGC 1334–1602 0.667 62.3
ycf23_p2 ycf23 AGGTTGTAAGCGCTGTGAAA GCTGAGAAATTCTTGTAGCAGC 1335–1603 0.667 62.3
ycf23_p3 ycf23 GGTTGTAAGCGCTGTGAAAC CGTCAAAACGCTGAGAAATTCT 1611 0.333 36.0
ycf23_p4 ycf23 AGGTTGTAAGCGCTGTGAAA CGTCAAAACGCTGAGAAATTCT 1612 0.333 36.0
ycf23_p5 ycf23 CTCAATGTGTACGTGCATGC GCTGAGAAATTCTTGTAGCAGC 1706 0.333 35.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Gracilariopsis longissima NC_039143.1 181896 View on NCBI ↗
Gracilariopsis mclachlanii NC_039144.1 184980 View on NCBI ↗
Gracilariopsis tenuifrons NC_058670.1 184308 View on NCBI ↗