Markers + reference

Porella

3 species · Porellaceae · Porellales

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Species 3
Genome length 121–122 kb
Candidate markers 270
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps7 Genome 468 0.0285 1.00 59.2 yes View details
psaM-trnS-GCU Genome 388 0.0685 0.94 81.5 yes View details
psbI-psbK Genome 332 0.0713 1.00 80.8 yes View details
chlB-trnK Genome 683 0.0444 0.93 75.4 yes View details
trnE-UGA-trnT-GGU Genome 1252 0.0451 0.92 82.4 yes View details
rpl32-trnL-UAG Genome 786 0.0576 0.96 81.7 yes View details
ycf1 Genome 3198 0.0250 1.00 56.7 yes View details
psaJ-rpl33 Genome 151 0.0626 0.99 80.5 yes View details
trnT-UGU-trnL-UAA Genome 244 0.0558 0.95 79.2 yes View details
trnS-GCU-psbI Genome 35 0.0762 1.00 79.1 yes View details
trnV-GAC-rps12 Genome 622 0.0334 1.00 78.5 no View details
psbJ-psbL Genome 120 0.0667 1.00 77.7 yes View details
ycf1-chlN Genome 121 0.0639 0.99 77.7 yes View details
trnL-UAA-trnF-GAA Genome 97 0.0550 1.00 76.2 yes View details
ycf66-petN Genome 84 0.0794 1.00 76.1 yes View details
trnR-UCU-trnG-GCC Genome 79 0.0591 1.00 75.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps7_p1 rps7 AATCGGATGTACGGTTTGGG TGGAAGACCCCAGTAAGGTT 967–1023 0.667 69.0
rps7_p2 rps7 AATCGGATGTACGGTTTGGG TTGGAAGACCCCAGTAAGGT 968–1024 0.667 69.0
rps7_p3 rps7 AGGGGGACATTAGATGCTGT TGGAAGACCCCAGTAAGGTT 1461–1520 0.667 67.8
rps7_p4 rps7 AGGGGGACATTAGATGCTGT TTGGAAGACCCCAGTAAGGT 1462–1521 0.667 67.8
rps7_p5 rps7 CAAGGGGACTAAAGCATGCT TGGAAGACCCCAGTAAGGTT 1309–1365 0.667 67.7
ycf66-petN_p1 ycf66-petN ATCGACTTGGATTTCGGGTG ATAAAACAAACGGCGGCATG 997–1005 1.000 83.6
ycf66-petN_p2 ycf66-petN ATCGACTTGGATTTCGGGTG AGGATCAAACCGTCATGCTC 871–876 1.000 83.6
ycf66-petN_p3 ycf66-petN ATCGACTTGGATTTCGGGTG GGATCAAACCGTCATGCTCT 870–875 1.000 83.6
ycf66-petN_p4 ycf66-petN ATCGACTTGGATTTCGGGTG TCGTATGGGGAAGAAGTGGT 536–538 1.000 83.3
ycf66-petN_p5 ycf66-petN ATCGACTTGGATTTCGGGTG GGGTGTCGCTTCATTTTTCG 931–934 0.667 68.8
trnR-UCU-trnG-GCC_p1 trnR-UCU-trnG-GCC GGATTCGAACCTATACTGGAGG TTCCAAGCTAATGATGCGGG 179 1.000 60.4
trnR-UCU-trnG-GCC_p2 trnR-UCU-trnG-GCC GGATTCGAACCTATACTGGAGG GCTAATGATGCGGGTTCGAT 173 1.000 59.2
trnR-UCU-trnG-GCC_p3 trnR-UCU-trnG-GCC GGATTCGAACCTATACTGGAGG CCAAGCTAATGATGCGGGTT 177 1.000 58.1
trnR-UCU-trnG-GCC_p4 trnR-UCU-trnG-GCC GGATTCGAACCTATACTGGAGG AATGATGCGGGTTCGATTCC 170 1.000 57.6
trnR-UCU-trnG-GCC_p5 trnR-UCU-trnG-GCC GGATTCGAACCTATACTGGAGG AAGCTAATGATGCGGGTTCG 175 1.000 57.4
psaM-trnS-GCU_p1 psaM-trnS-GCU CGTTACAGGTATTTTGGCCC GCTCGTACAACGGATTAGCA 466–490 1.000 79.7
psaM-trnS-GCU_p2 psaM-trnS-GCU CGTTACAGGTATTTTGGCCCT GCTCGTACAACGGATTAGCA 466–490 1.000 79.1
psaM-trnS-GCU_p3 psaM-trnS-GCU TCGTTACAGGTATTTTGGCCC GCTCGTACAACGGATTAGCA 467–491 1.000 79.1
psaM-trnS-GCU_p4 psaM-trnS-GCU CGTTACAGGTATTTTGGCCC AGCTCGTACAACGGATTAGC 467–491 1.000 78.7
psaM-trnS-GCU_p5 psaM-trnS-GCU CGTTACAGGTATTTTGGCCCT AGCTCGTACAACGGATTAGC 467–491 1.000 78.2
trnS-GCU-psbI_p1 trnS-GCU-psbI GCTATTCGTACCGAGGGTTC CGTAATCCAGGACGTAAAGAGT 96 1.000 63.3
trnS-GCU-psbI_p2 trnS-GCU-psbI TGCTAATCCGTTGTACGAGC CGTAATCCAGGACGTAAAGAGT 114 1.000 63.2
trnS-GCU-psbI_p3 trnS-GCU-psbI GGGTTCGAATCCCTCTCTCT CGTAATCCAGGACGTAAAGAGT 82 1.000 63.2
trnS-GCU-psbI_p4 trnS-GCU-psbI AGCTATTCGTACCGAGGGTT CGTAATCCAGGACGTAAAGAGT 97 1.000 62.5
trnS-GCU-psbI_p5 trnS-GCU-psbI GCTAATCCGTTGTACGAGCT CGTAATCCAGGACGTAAAGAGT 113 1.000 62.3
psbI-psbK_p1 psbI-psbK GGATTACGTCCCGGATCATT GCTTTTGTTTGGCAAGCTTC 415–465 1.000 75.2
psbI-psbK_p2 psbI-psbK GGATTACGTCCCGGATCATT TTTGTTTGGCAAGCTTCTGT 412–462 1.000 72.7
psbI-psbK_p3 psbI-psbK GGATTACGTCCCGGATCATT GCTTTTGTTTGGCAAGCTTCT 415–465 1.000 71.8
psbI-psbK_p4 psbI-psbK GGATTACGTCCCGGATCATT TTTTGTTTGGCAAGCTTCTGT 413–463 1.000 70.6
psbI-psbK_p5 psbI-psbK GGATTACGTCCCGGATCATT TGTTTGGCAAGCTTCTGTAAG 410–460 1.000 67.6

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
Porella gracillima NC_082430.1 121867 View on NCBI ↗
Porella grandiloba NC_072065.1 121433 View on NCBI ↗
Porella perrottetiana NC_043780.1 121806 View on NCBI ↗