Markers + reference

Pleurozia

3 species · Pleuroziaceae · Pleuroziales

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Species 3
Genome length 118–118 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf66 Genome 924 0.0231 1.00 59.1 yes View details
atpI-atpH Genome 271 0.0498 0.96 77.1 yes View details
psbI-psbK Genome 331 0.0423 1.00 70.3 yes View details
psbZ Genome 189 0.0071 1.00 43.0 yes View details
trnM-CAU-trnV-GAC Genome 615 0.0217 1.00 61.7 yes View details
ndhF Genome 2094 0.0239 1.00 58.3 yes View details
ndhF-rpl21 Genome 347 0.0374 0.98 66.8 yes View details
rpl32-trnL-UAG Genome 1214 0.0318 0.99 68.8 yes View details
rps15 Genome 267 0.0150 1.00 47.3 yes View details
psbA-trnH-GUG Genome 153 0.0697 1.00 79.3 yes View details
psbC-trnS-UGA Genome 117 0.0684 1.00 79.3 yes View details
rps19-rpl2 Genome 38 0.0702 1.00 79.0 yes View details
psaJ-rpl33 Genome 14 0.1429 1.00 78.6 yes View details
petG-trnW-CCA Genome 85 0.0510 1.00 78.4 yes View details
rpoA-rps11 Genome 23 0.0870 1.00 77.8 yes View details
trnM-CAU-atpE Genome 61 0.0656 1.00 77.7 yes View details
petB-petD Genome 110 0.0710 0.98 77.6 yes View details
rpl14-rpl16 Genome 128 0.0703 1.00 77.6 yes View details
psbZ-trnG-GCC Genome 224 0.0551 1.00 76.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf66_p1 ycf66 AAGCATGGAGGTTCGAATCC AAGTGGTAAGGCAGAGGACT 1946–1959 1.000 82.7
ycf66_p2 ycf66 GCCTTGGTGGTGAAATGGTA AAGTGGTAAGGCAGAGGACT 1995–2008 1.000 82.3
ycf66_p3 ycf66 AAGCATGGAGGTTCGAATCC GTGACATGGCCAAGTGGTAA 1957–1970 1.000 82.2
ycf66_p4 ycf66 AAGCATGGAGGTTCGAATCC CAAGTGGTAAGGCAGAGGAC 1947–1960 1.000 82.2
ycf66_p5 ycf66 ATGTGCAAACCGCTAGTCAA AAGTGGTAAGGCAGAGGACT 1611 0.333 52.2
atpI-atpH_p1 atpI-atpH AGGAGAATCTATGGAGGGTCA GCAGCAATAACAGAAGCAGC 327–348 1.000 71.1
atpI-atpH_p2 atpI-atpH AGGAGAATCTATGGAGGGTCA AGCAGCAGAAATCAAAGGGT 313–334 1.000 69.8
atpI-atpH_p3 atpI-atpH AGGAGAATCTATGGAGGGTCA CCAGCAGCAATAACAGAAGC 330–351 1.000 67.3
atpI-atpH_p4 atpI-atpH AGGAGAATCTATGGAGGGTCAT GCAGCAATAACAGAAGCAGC 327–348 1.000 67.1
atpI-atpH_p5 atpI-atpH GGAGAATCTATGGAGGGTCA GCAGCAATAACAGAAGCAGC 326–347 1.000 66.3
psbI-psbK_p1 psbI-psbK CCAAAAACAAAAAGGGAAACA TTTGTTTGGCAAGCTTCTGT 422–436 1.000 45.4
psbI-psbK_p2 psbI-psbK CCAAAAACAAAAAGGGAAACAA TTTGTTTGGCAAGCTTCTGT 422–436 1.000 45.4
psbI-psbK_p3 psbI-psbK CCAAAAACAAAAAGGGAAACAAA TTTGTTTGGCAAGCTTCTGT 422–436 1.000 45.4
psbI-psbK_p4 psbI-psbK CCAAAAACAAAAAGGGAAACA TGTTTGGCAAGCTTCTGTAAG 420–434 1.000 45.4
psbI-psbK_p5 psbI-psbK CCAAAAACAAAAAGGGAAACA GTTTGGCAAGCTTCTGTAAGT 419–433 1.000 45.4
psbA-trnH-GUG_p1 psbA-trnH-GUG GCTCCAGCTGTTAACGGTTA CTGCCTTAATCCACTTGGCT 199–213 1.000 84.9
psbA-trnH-GUG_p2 psbA-trnH-GUG GCTCCAGCTGTTAACGGTTA ACTGCCTTAATCCACTTGGC 200–214 1.000 84.6
psbA-trnH-GUG_p3 psbA-trnH-GUG GCTCCAGCTGTTAACGGTTA GATCCACAATCCACTGCCTT 212–226 1.000 84.5
psbA-trnH-GUG_p4 psbA-trnH-GUG TGAACGTAACGCTCACAACT CTGCCTTAATCCACTTGGCT 245–259 1.000 82.6
psbA-trnH-GUG_p5 psbA-trnH-GUG TGAACGTAACGCTCACAACT GATCCACAATCCACTGCCTT 258–272 1.000 82.4
psbC-trnS-UGA_p1 psbC-trnS-UGA ACTTTCTATGACTCCTCTTAATT TTCGAATCCCTCTCTCTCCT 162 1.000 48.4
psbC-trnS-UGA_p2 psbC-trnS-UGA ACTTTCTATGACTCCTCTTAATT GGTTCGAATCCCTCTCTCTC 164 1.000 48.3
psbC-trnS-UGA_p3 psbC-trnS-UGA ACTTTCTATGACTCCTCTTAATT GTTCGAATCCCTCTCTCTCC 163 1.000 48.3
psbC-trnS-UGA_p4 psbC-trnS-UGA ACTTTCTATGACTCCTCTTAATT GGGTTCGAATCCCTCTCTCT 165 1.000 48.2
psbC-trnS-UGA_p5 psbC-trnS-UGA ACTTTCTATGACTCCTCTTAATTA GGGTTCGAATCCCTCTCTCT 165 1.000 48.2
psbZ_p1 psbZ GATCTTCGTGCTCCATGGTT CGGAGTAGAGCAGTCTGGTA 1248–1263 1.000 83.1
psbZ_p2 psbZ GATCTTCGTGCTCCATGGTT AGTCGTCTTCATCGTCGTTG 1474–1490 1.000 82.8
psbZ_p3 psbZ GATCTTCGTGCTCCATGGTT CAAGTCGTCTTCATCGTCGT 1476–1492 1.000 82.8
psbZ_p4 psbZ CGTTTTTGGGATCTTCGTGC AGTCGTCTTCATCGTCGTTG 1483–1499 1.000 82.8
psbZ_p5 psbZ CGTTTTTGGGATCTTCGTGC CAAGTCGTCTTCATCGTCGT 1485–1501 1.000 82.8

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
Pleurozia acinosa NC_082059.1 118233 View on NCBI ↗
Pleurozia gigantea NC_082060.1 118423 View on NCBI ↗
Pleurozia subinflata NC_081020.1 118441 View on NCBI ↗