Markers + reference

Bryopsis

2 species · Bryopsidaceae · Bryopsidales

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Species 2
Genome length 107–153 kb
Candidate markers 222
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 222 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn16-trnS Genome 7018 0.4240 0.53 67.5 yes View details
trnS-psaJ Genome 21215 0.4413 0.61 67.6 yes View details
trnR-trnA Genome 82 0.6000 0.06 52.8 yes View details
trnR-rpoB Genome 12251 0.4300 0.37 64.9 yes View details
trnL-rrn5 Genome 3444 0.4711 0.59 69.8 no View details
ccsA Genome 1014 0.1059 0.97 82.0 yes View details
rpl12-cysT Genome 682 0.1411 0.98 81.9 yes View details
chlL-ccsA Genome 477 0.1111 0.94 81.0 yes View details
atpA Genome 2508 0.1337 0.96 80.7 yes View details
cemA Genome 918 0.0991 1.00 80.3 yes View details
chlB Genome 1518 0.1018 0.99 80.0 yes View details
rpl36-infA Genome 54 0.1800 0.93 79.8 yes View details
rpl23 Genome 642 0.1087 0.99 79.8 yes View details
psbZ-psbD Genome 1178 0.0997 1.00 79.8 yes View details
psbT-psbH Genome 501 0.1010 0.97 79.6 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpA_p1 atpA GAGCTGATCTCCACGTTTGT AGAAAATCGTTACGATGGACT 2865–2929 1.000 59.5
atpA_p2 atpA GAGCTGATCTCCACGTTTGT TCGTTACGATGGACTATTTCA 2859–2923 1.000 55.2
atpA_p3 atpA TTAACTAACCGACGCTCTAC AGGGAAAAAGAGGCCATTGA 2991 0.500 25.5
atpA_p4 atpA AATTAACTAACCGACGCTCT AGGGAAAAAGAGGCCATTGA 2993 0.500 24.2
atpA_p5 atpA TGAAAATTAACTAACCGACGCTC AGGGAAAAAGAGGCCATTGA 2997 0.500 23.8
rpl12-cysT_p1 rpl12-cysT TGCCCGGTGAAGATCAAAAA GACCAAGCCGCTTCTTCTAA 1370–1373 1.000 88.1
rpl12-cysT_p2 rpl12-cysT TGCCCGGTGAAGATCAAAAA CTAATGACCAAGCCGCTTCT 1378 0.500 59.7
rpl12-cysT_p3 rpl12-cysT GGCGCGAAAGTCAAAATTCA CTAATGACCAAGCCGCTTCT 1205 0.500 59.4
rpl12-cysT_p4 rpl12-cysT CAGGCGCGAAAGTCAAAATT CTAATGACCAAGCCGCTTCT 1207 0.500 59.4
rpl12-cysT_p5 rpl12-cysT TGCCCGGTGAAGATCAAAAA ATTCACCAATCGCACGAGAA 1480 0.500 59.2
rpl36-infA_p1 rpl36-infA ACAGAGGCACGTATTTTCAT TATGATTTAACACGTGGGCG 121–125 1.000 50.9
rpl36-infA_p2 rpl36-infA ACAGAGGCACGTATTTTCAT ATATGATTTAACACGTGGGCG 122–126 1.000 48.4
rpl36-infA_p3 rpl36-infA TACAGAGGCACGTATTTTCA TATGATTTAACACGTGGGCG 122–126 1.000 48.4
rpl36-infA_p4 rpl36-infA ACAGAGGCACGTATTTTCAT CATATGATTTAACACGTGGGCG 123–127 1.000 48.3
rpl36-infA_p5 rpl36-infA ACAGAGGCACGTATTTTCAT CCATATGATTTAACACGTGGGC 124–128 1.000 48.3
rpl23_p1 rpl23 CCCGAGTCCTCCTAGCATTA ATGCATGTATGGCTGAGTGG 1460 0.500 59.8
rpl23_p2 rpl23 CCGTGTACCTGGTGTATGTG ATGCATGTATGGCTGAGTGG 947 0.500 59.8
rpl23_p3 rpl23 CCCGAGTCCTCCTAGCATTA AAAAGCGGCGGACTCATAAT 1438 0.500 59.7
rpl23_p4 rpl23 CCGTGTACCTGGTGTATGTG AAAAGCGGCGGACTCATAAT 925 0.500 59.7
rpl23_p5 rpl23 CAAACGTTTATGCCCACCAC ATGCATGTATGGCTGAGTGG 1088 0.500 59.3
chlB_p1 chlB CGGGATAGCTCAGTGGTAGA AAGAAGTCCGCCTAATGCTG 2950–2951 1.000 88.5
chlB_p2 chlB GTGGGAGGATTCGAACCTTC AAGAAGTCCGCCTAATGCTG 2831–2834 1.000 88.4
chlB_p3 chlB TCAAAAAGCCGGGATAGCTC AAGAAGTCCGCCTAATGCTG 2959–2960 1.000 88.4
chlB_p4 chlB AAAAGAGCTGAGCTGCTTGT AAGAAGTCCGCCTAATGCTG 2306–2307 1.000 87.5
chlB_p5 chlB ACACTTCAAAAAGCCGGGAT AAGAAGTCCGCCTAATGCTG 2965 0.500 59.7
psbZ-psbD_p1 psbZ-psbD AATGGGTTGGCTTCGTGATT TCGAACCAACCTCTCTCTGT 1845–1848 1.000 86.8
psbZ-psbD_p2 psbZ-psbD GTATGGGCGTGGATGTTCTT TCGAACCAACCTCTCTCTGT 1763 0.500 59.7
psbZ-psbD_p3 psbZ-psbD GTATGGGCGTGGATGTTCTT TAGCGGCAACTCCAAAACTT 2248 0.500 59.5
psbZ-psbD_p4 psbZ-psbD GTATGGGCGTGGATGTTCTT ATCGCGTTATACGGTCGAAG 2147 0.500 59.5
psbZ-psbD_p5 psbZ-psbD AATGGGTTGGCTTCGTGATT TAGCGGCAACTCCAAAACTT 2333 0.500 59.2

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
Bryopsis hypnoides NC_013359.1 153429 View on NCBI ↗
Bryopsis plumosa NC_026795.1 106859 View on NCBI ↗