Markers + reference

Pohlia

3 species · Mniaceae · Bryales

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Species 3
Genome length 125–125 kb
Candidate markers 255
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbJ-petA Genome 996 0.0505 1.00 76.5 yes View details
cemA Genome 1506 0.0321 1.00 65.6 yes View details
ycf2 Genome 6924 0.0319 1.00 58.2 yes View details
trnK-UUU-chlB Genome 699 0.0573 0.96 82.4 yes View details
psbK-psbI Genome 500 0.0527 1.00 76.8 yes View details
trnR-UCU-atpA Genome 342 0.1101 1.00 78.1 yes View details
trnC-GCA-ycf66 Genome 501 0.0522 0.99 79.1 yes View details
rpl32-trnP-GGG Genome 255 0.0801 1.00 78.3 yes View details
ndhE-ndhI Genome 760 0.0487 0.99 75.9 yes View details
ycf1 Genome 4812 0.0325 1.00 58.8 yes View details
rrn4.5-rrn5 Genome 199 0.0570 1.00 81.5 yes View details
rrn5-rrn4.5 Genome 199 0.0570 1.00 81.5 yes View details
trnfM-CAU-trnG-UCC Genome 148 0.0608 1.00 81.4 yes View details
psbD-trnT-GGU Genome 629 0.0461 1.00 80.0 yes View details
rpl2-rps19 Genome 54 0.0741 1.00 79.9 yes View details
chlN-trnN-GUU Genome 1729 0.0383 0.99 79.4 yes View details
psbI-trnS-GCU Genome 105 0.0635 1.00 79.3 yes View details
ndhJ-trnF-GAA Genome 220 0.0645 0.99 78.9 yes View details
trnH-GUG-psbA Genome 131 0.1196 1.00 78.5 yes View details
cemA-ycf4 Genome 119 0.0833 0.97 78.1 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl2-rps19_p1 rpl2-rps19 CGTCGTCGTAAAAATGGATA TGATCAGCTACAAAAGGGCC 114–117 1.000 49.5
rpl2-rps19_p2 rpl2-rps19 TGATCCTTTAATTTTACGTCGTCG TGATCAGCTACAAAAGGGCC 130–133 1.000 49.3
rpl2-rps19_p3 rpl2-rps19 CGTCGTCGTAAAAATGGATAA TGATCAGCTACAAAAGGGCC 114–117 1.000 48.3
rpl2-rps19_p4 rpl2-rps19 TCCTTTAATTTTACGTCGTCG TGATCAGCTACAAAAGGGCC 127–130 1.000 47.2
rpl2-rps19_p5 rpl2-rps19 TGATCCTTTAATTTTACGTCGTCG GATCAGCTACAAAAGGGCCT 129–132 1.000 46.9
psbJ-petA_p1 psbJ-petA ATGACGTTTTTGGAAGCCCT ACCTTCAGGACCCGAACTTA 1878–1880 1.000 84.1
psbJ-petA_p2 psbJ-petA ATGACGTTTTTGGAAGCCCT TACCTTCAGGACCCGAACTT 1879–1881 1.000 84.1
psbJ-petA_p3 psbJ-petA ATGACGTTTTTGGAAGCCCT CATTGTACCTTCAGGACCCG 1884–1886 1.000 84.1
psbJ-petA_p4 psbJ-petA ATGACGTTTTTGGAAGCCCT ATTGTACCTTCAGGACCCGA 1883–1885 1.000 83.9
psbJ-petA_p5 psbJ-petA GTGCATGGACTAGCTGTACC ACCTTCAGGACCCGAACTTA 1699–1701 0.667 69.1
cemA_p1 cemA AATACGACCGGTTGCTTCTC GGCATTTATCCTCGGCGTAT 2103–2130 1.000 84.4
cemA_p2 cemA GCACATACAATACGACCGGT GGCATTTATCCTCGGCGTAT 2111–2138 1.000 83.8
cemA_p3 cemA AATACGACCGGTTGCTTCTC TGAATGGCTTTGGGTAGAGC 2491–2518 0.667 68.8
cemA_p4 cemA GCACATACAATACGACCGGT TGAATGGCTTTGGGTAGAGC 2499–2526 0.667 68.2
cemA_p5 cemA CGGATATGCTTCGGAGATCG GGCATTTATCCTCGGCGTAT 2079 0.333 51.8
cemA-ycf4_p1 cemA-ycf4 ATTATGGCTTGCCAAGACCG GGCATTTATCCTCGGCGTAT 421–436 1.000 81.5
cemA-ycf4_p2 cemA-ycf4 ATTATGGCTTGCCAAGACCG TATTCGGTGCACTTGGGTTT 738–753 1.000 78.2
cemA-ycf4_p3 cemA-ycf4 ATTATGGCTTGCCAAGACCG TTATTCGGTGCACTTGGGTT 739–754 1.000 78.1
cemA-ycf4_p4 cemA-ycf4 ATTATGGCTTGCCAAGACCG AGAAGGCATTTATCCTCGGC 425–440 0.667 65.1
cemA-ycf4_p5 cemA-ycf4 ATTATGGCTTGCCAAGACCG TGAATGGCTTTGGGTAGAGC 809–824 0.667 64.2
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA TTTTTATGAGTTACAAGATGCTT AAGCCGGAATAGCTCAGTTG 309–323 1.000 48.6
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA GATTTTTATGAGTTACAAGATGCT AAGCCGGAATAGCTCAGTTG 311–325 1.000 48.5
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA GATTTTTATGAGTTACAAGATGCTT AAGCCGGAATAGCTCAGTTG 311–325 1.000 48.5
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA ATTTTTATGAGTTACAAGATGCT AAGCCGGAATAGCTCAGTTG 310–324 1.000 48.5
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA GATTTTTATGAGTTACAAGATGC AAGCCGGAATAGCTCAGTTG 311–325 1.000 48.5
trnfM-CAU-trnG-UCC_p1 trnfM-CAU-trnG-UCC TAGCTCGCAAGGCTCATAAC AATATGCGGGTTCGATTCCC 228–230 1.000 84.0
trnfM-CAU-trnG-UCC_p2 trnfM-CAU-trnG-UCC GTAGCTCGCAAGGCTCATAA AATATGCGGGTTCGATTCCC 229–231 1.000 83.9
trnfM-CAU-trnG-UCC_p3 trnfM-CAU-trnG-UCC GTAGCTCGCAAGGCTCATAA AAGGAGAATATGCGGGTTCG 235–237 1.000 82.7
trnfM-CAU-trnG-UCC_p4 trnfM-CAU-trnG-UCC TAGCTCGCAAGGCTCATAAC AAGGAGAATATGCGGGTTCG 234–236 1.000 82.7
trnfM-CAU-trnG-UCC_p5 trnfM-CAU-trnG-UCC TAGCTCGCAAGGCTCATAAC TTGCCAAGGAGAATATGCGG 239–241 1.000 82.0

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
Pohlia elongata OR099888.1 125023 View on NCBI ↗
Pohlia flexuosa OR113699.1 124826 View on NCBI ↗
Pohlia lutescens OR099887.1 124711 View on NCBI ↗