Markers + reference

Palmaria

2 species · Palmariaceae · Palmariales

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Species 2
Genome length 193–193 kb
Candidate markers 481
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 481 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS(tga)-psaD LSC 452 0.1951 1.00 76.6 yes View details
chlB LSC 3475 0.0636 1.00 70.6 yes View details
ycf92 LSC 795 0.0994 1.00 79.0 yes View details
orf768 LSC 2307 0.0832 1.00 75.1 yes View details
orf88-apcF LSC 560 0.1137 0.53 68.2 yes View details
psaM-rrs LSC 879 0.1981 0.98 83.1 yes View details
orf402 LSC 1203 0.0856 1.00 79.8 yes View details
orf441 LSC 1326 0.0928 1.00 78.1 yes View details
ycf23 LSC 849 0.0754 1.00 76.9 yes View details
ycf45 LSC 1629 0.0595 1.00 76.7 yes View details
trnC(gca)-trnL(taa) LSC 39 0.1538 1.00 76.6 yes View details
cfxQ-trnC(gca) LSC 55 0.1273 1.00 76.3 yes View details
cpcS LSC 459 0.1133 1.00 76.0 yes View details
psaD-chlB LSC 213 0.1455 1.00 75.6 yes View details
ycf80-ssrA LSC 765 0.0732 1.00 75.6 yes View details
atpB LSC 1425 0.0491 1.00 75.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf45_p1 ycf45 GGTTCATTTGGTGCAGGAGA GGAGAGGTGGTAGAGTTGGT 2468 1.000 83.5
ycf45_p2 ycf45 GGTTCATTTGGTGCAGGAGA TGGAGAGGTGGTAGAGTTGG 2469 1.000 83.5
ycf45_p3 ycf45 GGTTCATTTGGTGCAGGAGA TTTCAGCATCTTCATCCGGG 2304 0.500 58.9
ycf45_p4 ycf45 TGAGTTCAAATGAGTGCGCT TTTCAGCATCTTCATCCGGG 2059 0.500 58.7
ycf45_p5 ycf45 ATGTGCCAACCATAGGTGAC TTTCAGCATCTTCATCCGGG 2276 0.500 58.6
trnS(tga)-psaD_p1 trnS(tga)-psaD CCGCAAATTACACGTGCATT GATGGTCGTGAAGCAGCTAA 1283 0.500 59.7
trnS(tga)-psaD_p2 trnS(tga)-psaD CCCGGATGAAGATGCTGAAA GATGGTCGTGAAGCAGCTAA 732 0.500 59.6
trnS(tga)-psaD_p3 trnS(tga)-psaD ACCAACTCTACCACCTCTCC GATGGTCGTGAAGCAGCTAA 568 0.500 59.4
trnS(tga)-psaD_p4 trnS(tga)-psaD CCGCAAATTACACGTGCATT TACGCAATGTTCCGATGTGT 1881 0.500 59.1
trnS(tga)-psaD_p5 trnS(tga)-psaD ATAGCAACACAGTTCCGCAA GATGGTCGTGAAGCAGCTAA 1297 0.500 59.0
psaD-chlB_p1 psaD-chlB CCAGTACTCCCACCAAATGT ACCTGCGTACATCCAGTATG 299–300 1.000 73.8
psaD-chlB_p2 psaD-chlB CCAGTACTCCCACCAAATGT GGACCTGCGTACATCCAGTA 301–302 1.000 73.8
psaD-chlB_p3 psaD-chlB CCCACCAAATGTAGGAGAAGG ACCTGCGTACATCCAGTATG 291–292 1.000 72.8
psaD-chlB_p4 psaD-chlB CCCACCAAATGTAGGAGAAGG GGACCTGCGTACATCCAGTA 293–294 1.000 72.8
psaD-chlB_p5 psaD-chlB CACCAAATGTAGGAGAAGGCA ACCTGCGTACATCCAGTATG 289–290 1.000 72.3
chlB_p1 chlB CTCAGGGATGCTAAAGCGTT GTCCTATCGCTTGCTTCCAA 1132 0.500 59.6
chlB_p2 chlB CTCAGGGATGCTAAAGCGTT ACTTTTTCTTGCGAACCCCT 937 0.500 59.2
chlB_p3 chlB CTCAGGGATGCTAAAGCGTT CGGTCTCTTTCCAGCATTGA 868 0.500 59.0
chlB_p4 chlB CTCAGGGATGCTAAAGCGTT GCTGCCCTGTCTACAAAGTT 1054 0.500 58.9
chlB_p5 chlB ATCTTAGCCTCAGGGATGCT GTCCTATCGCTTGCTTCCAA 1140 0.500 58.9
orf441_p1 orf441 CAGGGCGTTGCTCTTTATCT GTCCTATCGCTTGCTTCCAA 2140–2141 1.000 85.7
orf441_p2 orf441 CAGGGCGTTGCTCTTTATCT CGGTCTCTTTCCAGCATTGA 1876–1877 1.000 85.4
orf441_p3 orf441 TCGTGCGACTTGTTCATGAT GTCCTATCGCTTGCTTCCAA 2246–2247 1.000 85.1
orf441_p4 orf441 ACACATCGGAACATTGCGTA GTCCTATCGCTTGCTTCCAA 2326–2327 1.000 84.9
orf441_p5 orf441 CAGGGCGTTGCTCTTTATCT ACTTTTTCTTGCGAACCCCT 1945 0.500 59.2
atpB_p1 atpB GTCTGGTGCAATCACTCGTA TGTCTTTTTACATTCATTGCTCA 1528–1530 1.000 43.7
atpB_p2 atpB GTCTGGTGCAATCACTCGTA GTTGTCTTTTTACATTCATTGCTCA 1530–1532 1.000 43.7
atpB_p3 atpB GTCTGGTGCAATCACTCGTA TGAGTTGTCTTTTTACATTCATTGC 1533–1535 1.000 43.7
atpB_p4 atpB TCTGTCTGGTGCAATCACTC TGTCTTTTTACATTCATTGCTCA 1531–1533 1.000 43.7
atpB_p5 atpB GTCTGGTGCAATCACTCGTA CTGAGTTGTCTTTTTACATTCATTGC 1534–1536 1.000 43.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Palmaria decipiens NC_046495.1 193007 View on NCBI ↗
Palmaria palmata NC_031147.1 192960 View on NCBI ↗