Markers + reference

Stephanodiscus

3 species · Stephanodiscaceae · Stephanodiscales

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Species 3
Genome length 130–130 kb
Candidate markers 347
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 347 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbX-rbcS LSC 403 0.0265 1.00 66.9 yes View details
psaE LSC 198 0.0067 1.00 30.7 yes View details
ycf45-trnF(gaa) LSC 1377 0.0286 1.00 68.3 yes View details
petA-chlI LSC 514 0.0246 1.00 53.6 yes View details
ftsH-trnT(tgt) LSC 266 0.0276 1.00 57.0 yes View details
thiS-psbW SSC 541 0.0222 1.00 62.6 yes View details
dnaK SSC 1797 0.0085 1.00 50.0 yes View details
rpl3 SSC 624 0.0118 1.00 53.9 yes View details
cbbX-ycf39 LSC 27 0.0988 1.00 81.5 yes View details
ycf35-psaC IRb 92 0.0580 1.00 71.3 yes View details
groEL-dnaK SSC 90 0.0593 1.00 71.3 yes View details
psaC-ycf35 IRa 92 0.0580 1.00 71.3 yes View details
trnR(tct)-psaE LSC 177 0.0343 0.99 69.0 yes View details
rpoC1-rpoB LSC 9 0.0741 1.00 68.9 yes View details
petB LSC 648 0.0103 1.00 65.3 yes View details
trnV(tac)-trnR(tct) LSC 13 0.0513 1.00 64.7 yes View details
ycf4 LSC 546 0.0098 1.00 63.9 yes View details
orf131 SSC 396 0.0084 1.00 59.9 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
psbX-rbcS_p1 psbX-rbcS CCTGCTGTTAAACTCGCGAT CCAGCTAACGAACCAGGTTT 561 1.000 76.3
psbX-rbcS_p2 psbX-rbcS CCTGCTGTTAAACTCGCGAT TTAGATCGTACAGAAGGCGC 537 1.000 73.4
psbX-rbcS_p3 psbX-rbcS ACGCTCTACACGATCAGTTT CCAGCTAACGAACCAGGTTT 628 1.000 73.1
psbX-rbcS_p4 psbX-rbcS CCTGCTGTTAAACTCGCGAT TAGATCGTACAGAAGGCGCA 536 1.000 72.4
psbX-rbcS_p5 psbX-rbcS GTACGCTCTACACGATCAGT CCAGCTAACGAACCAGGTTT 630 1.000 72.3
trnV(tac)-trnR(tct)_p1 trnV(tac)-trnR(tct) AACTCAGCGGTAGAGTGTCT TGTCCTGATCCGTTAGACGA 104 1.000 79.1
trnV(tac)-trnR(tct)_p2 trnV(tac)-trnR(tct) GAGTGTCTGCCTTACAAGCA TGTCCTGATCCGTTAGACGA 92 1.000 78.6
trnV(tac)-trnR(tct)_p3 trnV(tac)-trnR(tct) GCCTTACAAGCAGAAGGTCA TGTCCTGATCCGTTAGACGA 84 1.000 78.5
trnV(tac)-trnR(tct)_p4 trnV(tac)-trnR(tct) TGCCTTACAAGCAGAAGGTC TGTCCTGATCCGTTAGACGA 85 1.000 78.5
trnV(tac)-trnR(tct)_p5 trnV(tac)-trnR(tct) CAAGCAGAAGGTCACAGGTT TAGGCCCAGTAGGAATCGAA 124 1.000 76.7
trnR(tct)-psaE_p1 trnR(tct)-psaE TCGTCTAACGGATCAGGACA TGATCCACTGTTGCAACTGT 323–329 1.000 80.0
trnR(tct)-psaE_p2 trnR(tct)-psaE TCGTCTAACGGATCAGGACA TCCACTGTTGCAACTGTTCC 320–326 1.000 77.9
trnR(tct)-psaE_p3 trnR(tct)-psaE TTCGATTCCTACTGGGCCTA TGATCCACTGTTGCAACTGT 277–283 1.000 77.8
trnR(tct)-psaE_p4 trnR(tct)-psaE CGTCTAACGGATCAGGACAG TGATCCACTGTTGCAACTGT 322–328 1.000 77.1
trnR(tct)-psaE_p5 trnR(tct)-psaE TCGTCTAACGGATCAGGACA CCACTTTGATCCACTGTTGC 329–335 1.000 77.0
psaE_p1 psaE CAAGCAGAAGGTCACAGGTT TCCAATTTGCAGGACAAGCT 1173–1180 1.000 81.6
psaE_p2 psaE GCAGAAGGTCACAGGTTCAA TCCAATTTGCAGGACAAGCT 1170–1177 1.000 81.6
psaE_p3 psaE AACTCAGCGGTAGAGTGTCT TCCAATTTGCAGGACAAGCT 1199–1206 1.000 81.1
psaE_p4 psaE TACGCCCGTTAAATGCTGAA TCCAATTTGCAGGACAAGCT 1552–1559 1.000 80.9
psaE_p5 psaE TTACGCCCGTTAAATGCTGA TCCAATTTGCAGGACAAGCT 1553–1560 1.000 80.9
ycf45-trnF(gaa)_p1 ycf45-trnF(gaa) TCAGAGAAGCATTTACCAAA TCCACTGCTCTACCAACTGA 1458–1460 1.000 43.3
ycf45-trnF(gaa)_p2 ycf45-trnF(gaa) TCAGAGAAGCATTTACCAAA TGGAGACACGAGGATCTTCA 1479–1481 1.000 43.3
ycf45-trnF(gaa)_p3 ycf45-trnF(gaa) TCAGAGAAGCATTTACCAAA AACTGGAGACACGAGGATCT 1482–1484 1.000 43.3
ycf45-trnF(gaa)_p4 ycf45-trnF(gaa) TCAGAGAAGCATTTACCAAA ACTGGAGACACGAGGATCTT 1481–1483 1.000 43.3
ycf45-trnF(gaa)_p5 ycf45-trnF(gaa) ATCAGAGAAGCATTTACCAA TCCACTGCTCTACCAACTGA 1459–1461 1.000 43.3
rpoC1-rpoB_p1 rpoC1-rpoB AGGTAATTTTCTCTGGGACCA TGATGAGTTTAGTTCAGACGA 214 1.000 40.4
rpoC1-rpoB_p2 rpoC1-rpoB TCTCTGGGACCATTGTAAGA TGATGAGTTTAGTTCAGACGA 205 1.000 40.4
rpoC1-rpoB_p3 rpoC1-rpoB AGGTAATTTTCTCTGGGACCA TGATGAGTTTAGTTCAGACGAA 214 1.000 40.4
rpoC1-rpoB_p4 rpoC1-rpoB AGGTAATTTTCTCTGGGACCA TTGATGAGTTTAGTTCAGACGA 215 1.000 40.4
rpoC1-rpoB_p5 rpoC1-rpoB TTCTCTGGGACCATTGTAAGA TGATGAGTTTAGTTCAGACGA 206 1.000 40.4

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
Stephanodiscus hantzschii PV577938.1 129553 View on NCBI ↗
Stephanodiscus hantzschii f. tenuis OR666652.1 129553 View on NCBI ↗
Stephanodiscus minutulus PV423684.1 129555 View on NCBI ↗