Markers + reference

Grateloupia

3 species · Halymeniaceae · Halymeniales

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Species 3
Genome length 189–196 kb
Candidate markers 467
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 467 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn16-ompR Genome 1784 0.2835 0.85 79.4 yes View details
ompR-psbD Genome 3474 0.2100 0.30 64.7 yes View details
rpl11-trnW-CCA Genome 1341 0.2673 0.97 83.3 yes View details
moeB-rpl9 Genome 1771 0.1940 0.08 57.1 yes View details
clpC-rpl19 Genome 1031 0.2139 0.70 75.3 yes View details
orf12-trnG-UCC Genome 650 0.2545 0.99 83.1 yes View details
ycf22-psaC Genome 725 0.1591 0.94 83.4 yes View details
cpeA-ccsA Genome 570 0.2244 0.97 82.9 yes View details
ycf80-trnR-CCG Genome 967 0.1437 0.99 80.5 yes View details
trnN-GUU-trnL-UAG Genome 172 0.1575 0.95 80.5 yes View details
syh Genome 1257 0.0994 1.00 79.7 yes View details
trnG-UCC-pafII Genome 80 0.1772 0.99 79.7 yes View details
rps5 Genome 528 0.0803 0.98 79.5 yes View details
ycf53 Genome 720 0.1037 1.00 79.4 yes View details
ycf38 Genome 876 0.0909 1.00 79.4 yes View details
atpB Genome 1422 0.0699 1.00 79.4 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf80-trnR-CCG_p1 ycf80-trnR-CCG AAATGTCTGTGTGGCTGTGT CGGTCGAAGGTTCAAATCCT 1204 0.333 52.1
ycf80-trnR-CCG_p2 ycf80-trnR-CCG AAATGTCTGTGTGGCTGTGT TTGGGCATGTAACTCAGTGG 1249 0.333 51.3
ycf80-trnR-CCG_p3 ycf80-trnR-CCG AAATGTCTGTGTGGCTGTGT AGTTCGTTCATTGCAGGAGT 1900 0.333 48.5
ycf80-trnR-CCG_p4 ycf80-trnR-CCG AAATGTCTGTGTGGCTGTGT TGGGCATGTAACTCAGTGGA 1248 0.333 47.7
ycf80-trnR-CCG_p5 ycf80-trnR-CCG AAATGTCTGTGTGGCTGTGT GGGCATGTAACTCAGTGGAT 1247 0.333 47.1
cpeA-ccsA_p1 cpeA-ccsA CGGCGGAAAAACTAGCTAGT AATGGACGGCAGTTAATCCC 1206 0.333 52.9
cpeA-ccsA_p2 cpeA-ccsA CGGCGGAAAAACTAGCTAGT CCCATACAGCTCCAGCAATT 1671 0.333 52.8
cpeA-ccsA_p3 cpeA-ccsA GCGCCTAATCAACTACTGCT AATGGACGGCAGTTAATCCC 1055 0.333 52.4
cpeA-ccsA_p4 cpeA-ccsA GCGATAGAGTTTCTGCTGCT AATGGACGGCAGTTAATCCC 1470 0.333 52.4
cpeA-ccsA_p5 cpeA-ccsA GCGCCTAATCAACTACTGCT CCCATACAGCTCCAGCAATT 1520 0.333 52.4
ycf22-psaC_p1 ycf22-psaC AAACGGGGATCATCAAGACG CCCTCAGAGGATAAAACGGC 1561 0.333 52.8
ycf22-psaC_p2 ycf22-psaC AAACGGGGATCATCAAGACG GGACGTAACATAGGTGCAGG 1801 0.333 52.6
ycf22-psaC_p3 ycf22-psaC AAACGGGGATCATCAAGACG GGTCAAGCAGGACGTAACAT 1810 0.333 52.4
ycf22-psaC_p4 ycf22-psaC AAACGGGGATCATCAAGACG TGGAACGGATGTAAAGCTGG 1219 0.333 52.3
ycf22-psaC_p5 ycf22-psaC AAACGGGGATCATCAAGACG GGAACGGATGTAAAGCTGGT 1218 0.333 52.3
trnN-GUU-trnL-UAG_p1 trnN-GUU-trnL-UAG CTACCACTGAGCTACTGAGGA AGCGTGTCTACCAATTCCAC 213–222 1.000 82.5
trnN-GUU-trnL-UAG_p2 trnN-GUU-trnL-UAG TCTACCACTGAGCTACTGAGG AGCGTGTCTACCAATTCCAC 214–223 1.000 82.5
trnN-GUU-trnL-UAG_p3 trnN-GUU-trnL-UAG CTACCACTGAGCTACTGAGGA CTACCAATTCCACCACGTCC 206–215 1.000 81.3
trnN-GUU-trnL-UAG_p4 trnN-GUU-trnL-UAG TCTACCACTGAGCTACTGAGG CTACCAATTCCACCACGTCC 207–216 1.000 81.3
trnN-GUU-trnL-UAG_p5 trnN-GUU-trnL-UAG ACCAATCGGTTAACAGCCG AGCGTGTCTACCAATTCCAC 238–247 1.000 81.0
ycf53_p1 ycf53 AAATTCATTGACCAGCCCGA GGTCCAGGAGATCCATCTGT 1882–1883 1.000 84.7
ycf53_p2 ycf53 AATTCATTGACCAGCCCGAA GGTCCAGGAGATCCATCTGT 1881–1882 1.000 84.7
ycf53_p3 ycf53 AATTCATTGACCAGCCCGAA TGGTCCAGGAGATCCATCTG 1882–1883 1.000 84.7
ycf53_p4 ycf53 TCCAAGTCGGCAATTCAGTC GGTCCAGGAGATCCATCTGT 1698 0.333 50.2
ycf53_p5 ycf53 TCCAAGTCGGCAATTCAGTC TGGTCCAGGAGATCCATCTG 1699 0.333 50.2
rrn16-ompR_p1 rrn16-ompR CATTGCGGAAAATTCCCCAC TGCTCCTAGTTCTAGTCCGG 2344 0.333 52.8
rrn16-ompR_p2 rrn16-ompR CATTGCGGAAAATTCCCCAC GCTCCTAGTTCTAGTCCGGT 2343 0.333 52.8
rrn16-ompR_p3 rrn16-ompR AGCTACTGATCGTTGCCTTG TGCTCCTAGTTCTAGTCCGG 2259 0.333 52.8
rrn16-ompR_p4 rrn16-ompR CAGCTACTGATCGTTGCCTT TGCTCCTAGTTCTAGTCCGG 2260 0.333 52.8
rrn16-ompR_p5 rrn16-ompR AGCTACTGATCGTTGCCTTG GCTCCTAGTTCTAGTCCGGT 2258 0.333 52.8

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
Grateloupia asiatica NC_084248.1 189389 View on NCBI ↗
Grateloupia filicina NC_037841.1 195990 View on NCBI ↗
Grateloupia turuturu NC_066971.1 188575 View on NCBI ↗