Markers + reference

Gracilaria

17 species · Gracilariaceae · Gracilariales

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Species 17
Genome length 178–183 kb
Candidate markers 459
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 459 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn5-rps6 Genome 329 0.3499 0.94 72.3 yes View details
trpG-ccs1 Genome 343 0.3150 0.98 73.1 yes View details
ycf37 Genome 471 0.1880 1.00 82.0 yes View details
ycf23 Genome 807 0.1712 1.00 83.0 yes View details
orf671 Genome 2016 0.1916 1.00 83.4 yes View details
acpP Genome 264 0.2807 0.99 77.6 yes View details
petF Genome 294 0.2325 1.00 75.0 yes View details
dnaB Genome 1791 0.1577 1.00 80.2 yes View details
psbD-ompR Genome 1631 0.3566 0.77 76.0 yes View details
ompR-rns Genome 419 0.2373 0.91 74.1 no View details
orf196-trnM(cat) Genome 612 0.1095 1.00 85.1 yes View details
orf241 Genome 726 0.1762 1.00 84.9 yes View details
orf196 Genome 591 0.1444 1.00 84.2 yes View details
orf190 Genome 573 0.1808 1.00 84.1 yes View details
trnR(ccg)-orf441 Genome 772 0.1557 1.00 83.4 yes View details
ompR Genome 729 0.0896 1.00 83.1 yes View details
dsbD Genome 735 0.1667 1.00 82.3 yes View details
syfB-rps1 Genome 530 0.1006 0.98 82.3 yes View details
rbcL Genome 1467 0.0649 1.00 80.8 yes View details
ycf60 Genome 615 0.0810 1.00 80.7 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
rrn5-rps6_p1 rrn5-rps6 TTATAGCGCAGTGGAACCAC CCCTATACCAGACCGTCCAT 1009–1079 0.412 68.2
rrn5-rps6_p2 rrn5-rps6 ATCTCCCCCAAGAGTTCACA CCCTATACCAGACCGTCCAT 1500–1570 0.412 68.0
rrn5-rps6_p3 rrn5-rps6 TCTCCCCCAAGAGTTCACAT CCCTATACCAGACCGTCCAT 1499–1569 0.412 68.0
rrn5-rps6_p4 rrn5-rps6 CAAGTCGAGCAGAGACGAAA CCCTATACCAGACCGTCCAT 1600–1670 0.412 68.0
rrn5-rps6_p5 rrn5-rps6 AGGGAAGCTTTTTGGGAAGG CCCTATACCAGACCGTCCAT 936–1006 0.235 61.2
ycf60_p1 ycf60 AGGGAAGCTTTTTGGGAAGG GTAAACCTTGCCCAGAACCA 2025–2120 0.294 63.6
ycf60_p2 ycf60 AGGGAAGCTTTTTGGGAAGG TGTAAACCTTGCCCAGAACC 2026–2121 0.294 63.6
ycf60_p3 ycf60 AGGGAAGCTTTTTGGGAAGG GCCCAGAACCAATTGGAGAA 2016–2111 0.235 60.7
ycf60_p4 ycf60 GGTTTCTCCGCTTAAACCCA GTAAACCTTGCCCAGAACCA 1626–1631 0.118 46.0
ycf60_p5 ycf60 GGTTTCTCCGCTTAAACCCA TGTAAACCTTGCCCAGAACC 1627–1632 0.118 46.0
trpG-ccs1_p1 trpG-ccs1 TGGGAGTTATATCTGGGCGT TCTCAAATCTGGGTCAACAGT 1170–1174 0.118 31.3
trpG-ccs1_p2 trpG-ccs1 TGGGAGTTATATCTGGGCGT TGGTCATCCCAGATTCCTATCA 1440 0.059 25.1
trpG-ccs1_p3 trpG-ccs1 CAGCGCGTTATCACAGTTTG TGGTCATCCCAGATTCCTATCA 939 0.059 24.8
trpG-ccs1_p4 trpG-ccs1 TGGGAGTTATATCTGGGCGT GCAGGTTTCACTAATAGAGCCA 1128 0.059 24.6
trpG-ccs1_p5 trpG-ccs1 TGGGAGTTATATCTGGGCGT AGCAGGTTTCACTAATAGAGCC 1129 0.059 24.4
dsbD_p1 dsbD AATAGGAGCAATTCGGCCAG AGCGTGTCTACCAATTCCAC 1603–1658 0.941 87.2
dsbD_p2 dsbD AATAGGAGCAATTCGGCCAG TCAAATCCTTCCTGGGGAGT 1373–1400 0.941 87.1
dsbD_p3 dsbD AATAGGAGCAATTCGGCCAG TACATGCGGACAGAGAGACT 1661–1716 0.647 74.4
dsbD_p4 dsbD AATAGGAGCAATTCGGCCAG GGTTCAAATCCTTCCTGGGG 1376–1403 0.588 71.3
dsbD_p5 dsbD AGCGTACAAGCTCGTTTCTT TCAAATCCTTCCTGGGGAGT 1340–1353 0.118 48.4
ycf37_p1 ycf37 GTTCAAGTCCTGCTATCCCG CGAGCCCTAAAGCCAGATTT 689–738 0.824 84.1
ycf37_p2 ycf37 GTTCAAGTCCTGCTATCCCG TAGACTCATGCGAGCCCTAA 699–748 0.294 62.8
ycf37_p3 ycf37 GTTCAAGTCCTGCTATCCCG CTGGATAGACTCATGCGAGC 704–753 0.176 58.1
ycf37_p4 ycf37 GCTAAACGGGATATAGCGCA CGAGCCCTAAAGCCAGATTT 748–797 0.118 51.7
ycf37_p5 ycf37 TGCTAAACGGGATATAGCGC CGAGCCCTAAAGCCAGATTT 749–798 0.118 51.7
ycf23_p1 ycf23 GCAAAGCTGGTCAAATTGCA TTCTTGTTGCAGCTCTCACT 1667–1681 0.294 54.6
ycf23_p2 ycf23 TGCAAAGCTGGTCAAATTGC TTCTTGTTGCAGCTCTCACT 1668–1682 0.294 54.6
ycf23_p3 ycf23 AGAAATGGTTCCTTGGGACG TTCTTGTTGCAGCTCTCACT 1690–1704 0.235 51.6
ycf23_p4 ycf23 ACGTAGTATGGGGCTAGCAT TTCTTGTTGCAGCTCTCACT 1552–1560 0.118 48.5
ycf23_p5 ycf23 AGCGTGTCCAACAGACTTTT TTCTTGTTGCAGCTCTCACT 1600–1614 0.118 48.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Gracilaria baiana NC_058651.1 179484 View on NCBI ↗
Gracilaria birdiae NC_058652.1 183364 View on NCBI ↗
Gracilaria brevis PV464276.1 180862 View on NCBI ↗
Gracilaria bursa-pastoris NC_058653.1 181313 View on NCBI ↗
Gracilaria caudata NC_058654.1 183134 View on NCBI ↗
Gracilaria cearensis NC_058655.1 182079 View on NCBI ↗
Gracilaria cervicornis NC_058656.1 180132 View on NCBI ↗
Gracilaria cornea NC_058658.1 182454 View on NCBI ↗
Gracilaria crassissima NC_058659.1 181978 View on NCBI ↗
Gracilaria domingensis NC_058660.1 179662 View on NCBI ↗
Gracilaria isabellana NC_058662.1 181790 View on NCBI ↗
Gracilaria multipartita NC_058663.1 179145 View on NCBI ↗
Gracilaria ornata NC_058664.1 178896 View on NCBI ↗
Gracilaria pachydermatica NC_058665.1 179707 View on NCBI ↗
Gracilaria tikvahiae NC_058667.1 179992 View on NCBI ↗
Gracilaria urvillei NC_058668.1 178239 View on NCBI ↗
Gracilaria usneoides NC_058669.1 183376 View on NCBI ↗