Markers + reference

Mazzaella

2 species · Gigartinaceae · Gigartinales

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Species 2
Genome length 179–180 kb
Candidate markers 463
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 463 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf58-cemA Genome 2368 0.1060 1.00 77.6 yes View details
psbE-ycf63 Genome 712 0.0994 0.99 79.9 yes View details
clpC-rpl19 Genome 999 0.1251 1.00 80.8 yes View details
trnS(gct)-trnD(gtc) Genome 1650 0.1967 0.91 83.2 yes View details
cbbX-trnC(gca) Genome 90 0.1125 0.89 81.0 yes View details
ycf27-psbD Genome 447 0.0952 0.94 80.1 yes View details
pdhB-petA Genome 64 0.1207 0.91 79.6 yes View details
pbsA-rpl35 Genome 708 0.0919 1.00 79.4 yes View details
trnL(tag)-trnN(gtt) Genome 169 0.1488 0.99 79.1 yes View details
trnP(tgg)-ycf52 Genome 55 0.1636 1.00 78.8 yes View details
trnQ(ttg)-psb28 Genome 279 0.0993 0.97 77.8 yes View details
psaF-psaJ Genome 24 0.1304 0.96 77.7 yes View details
ycf80 Genome 1407 0.0839 1.00 77.6 yes View details
ccdA Genome 741 0.0850 1.00 77.3 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
pbsA-rpl35_p1 pbsA-rpl35 GAACCGAGATTCTGGTGGTC AGACTTGCTGCTTTGCTGTA 1692–1728 1.000 83.7
pbsA-rpl35_p2 pbsA-rpl35 GAACCGAGATTCTGGTGGTC GCAACAAATGACTGCGTGAA 1388 0.500 59.0
pbsA-rpl35_p3 pbsA-rpl35 ATTGGCAACCAGGTAATGCA GCAACAAATGACTGCGTGAA 1131 0.500 58.5
pbsA-rpl35_p4 pbsA-rpl35 AACGAACCGAGATTCTGGTG GCAACAAATGACTGCGTGAA 1391 0.500 58.4
pbsA-rpl35_p5 pbsA-rpl35 AACCCGGATGAAGTTTGTCC GCAACAAATGACTGCGTGAA 1156 0.500 58.3
pdhB-petA_p1 pdhB-petA TCTGTGAGGAAATTAGTAGCT CTTTGCTGTGACACTTGCAC 170–176 1.000 46.0
pdhB-petA_p2 pdhB-petA TCTGTGAGGAAATTAGTAGCT TCTTTGCTGTGACACTTGCA 171–177 1.000 46.0
pdhB-petA_p3 pdhB-petA TTCTGTGAGGAAATTAGTAGCT CTTTGCTGTGACACTTGCAC 171–177 1.000 46.0
pdhB-petA_p4 pdhB-petA AGATTCTGTGAGGAAATTAGTAGCT CTTTGCTGTGACACTTGCAC 174–180 1.000 45.9
pdhB-petA_p5 pdhB-petA AGATTCTGTGAGGAAATTAGTAGCT TCTTTGCTGTGACACTTGCA 175–181 1.000 45.8
ycf58-cemA_p1 ycf58-cemA TTGATGAGAGAGCCAGTTGC ACCTCTGCATTTGGATCGAG 2550 0.500 56.6
ycf58-cemA_p2 ycf58-cemA TTGATGAGAGAGCCAGTTGC CCTCTGCATTTGGATCGAGT 2549 0.500 56.6
ycf58-cemA_p3 ycf58-cemA GAGCCAGTTGCCTTCCATAT ACCTCTGCATTTGGATCGAG 2541 0.500 54.6
ycf58-cemA_p4 ycf58-cemA GAGCCAGTTGCCTTCCATAT CCTCTGCATTTGGATCGAGT 2540 0.500 54.6
ycf58-cemA_p5 ycf58-cemA AGAGCCAGTTGCCTTCCATA CCTCTGCATTTGGATCGAGT 2541 0.500 51.7
trnMe(cat)_p1 trnMe(cat) CCATCAGCAGTGGCAACTTA AACACGTATTGGTCAACCGT 2404 0.500 56.7
trnMe(cat)_p2 trnMe(cat) CCATCAGCAGTGGCAACTTA ACACGTATTGGTCAACCGTT 2403 0.500 56.7
trnMe(cat)_p3 trnMe(cat) CCATCAGCAGTGGCAACTTA CCCGCTACCCGCTTTAAATA 2147 0.500 56.7
trnMe(cat)_p4 trnMe(cat) AGCGATACAGCAAAGGCATT ACACGTATTGGTCAACCGTT 2619 0.500 56.1
trnMe(cat)_p5 trnMe(cat) AGCGATACAGCAAAGGCATT CCCGCTACCCGCTTTAAATA 2363 0.500 56.1
cbbX-trnC(gca)_p1 cbbX-trnC(gca) ACGATTTAGTAACTATACAATCAGA TCTGCCTTACCACTTGGCTA 161–176 1.000 48.3
cbbX-trnC(gca)_p2 cbbX-trnC(gca) ACGATTTAGTAACTATACAATCAGA TTGCAATCCTCTGCCTTACC 170–185 1.000 48.1
cbbX-trnC(gca)_p3 cbbX-trnC(gca) ACGATTTAGTAACTATACAATCAGA GGATTTGCAATCCTCTGCCT 174–189 1.000 48.0
cbbX-trnC(gca)_p4 cbbX-trnC(gca) ACGATTTAGTAACTATACAATCAGA AGGATTTGCAATCCTCTGCC 175–190 1.000 47.9
cbbX-trnC(gca)_p5 cbbX-trnC(gca) ACGATTTAGTAACTATACAATCAGA TTTTAGGCGGTACCCAGACT 209–224 1.000 47.3
ycf80_p1 ycf80 ACTAGGCATTGCACCAACAA AAACAAGGAGGTTGCTCTGG 2161–2177 1.000 85.6
ycf80_p2 ycf80 TTGCACCAACAATACCAGCT AAACAAGGAGGTTGCTCTGG 2153–2169 1.000 85.6
ycf80_p3 ycf80 GGCATTGCACCAACAATACC AAACAAGGAGGTTGCTCTGG 2157–2173 1.000 85.6
ycf80_p4 ycf80 ACCAGCTGCTCGACAATTAG AAACAAGGAGGTTGCTCTGG 2140–2156 1.000 85.5
ycf80_p5 ycf80 CCAGCTGCTCGACAATTAGT AAACAAGGAGGTTGCTCTGG 2139–2155 1.000 85.5

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
Mazzaella laminarioides OR881974.1 179093 View on NCBI ↗
Mazzaella membranacea OR909685.1 179761 View on NCBI ↗