Markers + reference

Coscinodiscus

3 species · Coscinodiscaceae · Coscinodiscales

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Species 3
Genome length 122–124 kb
Candidate markers 345
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 11 remaining regions by MarkerSeek score (out of 345 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rrn5 IRb 318 0.3977 0.46 66.1 yes View details
syfB SSC 2118 0.3747 0.54 71.9 yes View details
rrn5 IRa 318 0.3991 0.46 66.2 no View details
rpoB LSC 4215 0.1789 0.99 73.9 yes View details
rpoC2 LSC 4248 0.2064 1.00 73.7 yes View details
rns-trnI(gau) IRb 74 0.2342 1.00 81.4 yes View details
trnI(gau)-rns IRa 74 0.2342 1.00 81.4 yes View details
rpl20-acpP IRb 1670 0.1699 1.00 81.3 yes View details
acpP-rpl20 IRa 1670 0.1693 1.00 81.3 yes View details
bas1 IRb 612 0.1402 0.98 80.8 yes View details
rbcL LSC 1473 0.0706 1.00 79.7 yes View details
psbC LSC 1416 0.1073 1.00 79.7 yes View details
petA LSC 945 0.1386 1.00 79.7 yes View details
rpl2 SSC 828 0.1965 1.00 79.6 yes View details
trnL(uaa)-trnC(gca) SSC 68 0.4677 0.99 79.4 yes View details
bas1 IRa 612 0.1373 1.00 78.8 no 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
rbcL_p1 rbcL ATTCCAAGGTCCTGCAACAG GCACCTTCGTTACGAGCTAA 861 0.333 52.5
rbcL_p2 rbcL ATTCCAAGGTCCTGCAACAG AACACCAGACATACGCATCC 526 0.333 52.5
rbcL_p3 rbcL GCTGTTGCTGCTTTACGTTT GCACCTTCGTTACGAGCTAA 917 0.333 52.3
rbcL_p4 rbcL GCTGTTGCTGCTTTACGTTT AACACCAGACATACGCATCC 582 0.333 52.2
rbcL_p5 rbcL ATTCCAAGGTCCTGCAACAG TACCAACAACTGTACCAGCG 557 0.333 51.4
bas1_p1 bas1 GTTAGTCGCGGATCAACAGT GATGACCTTTGAAAGCGTGC 1054 0.333 53.0
bas1_p2 bas1 ATCAAACGGGAACAGTTGCT GATGACCTTTGAAAGCGTGC 1002 0.333 52.9
bas1_p3 bas1 GTTAGTCGCGGATCAACAGT CCGTTTTCGTGCTACGTTTC 1199 0.333 52.7
bas1_p4 bas1 GTTAGTCGCGGATCAACAGT CGTTTTCGTGCTACGTTTCC 1198 0.333 52.7
bas1_p5 bas1 ATCAAACGGGAACAGTTGCT CGTTTTCGTGCTACGTTTCC 1146 0.333 52.6
rpl20-acpP_p1 rpl20-acpP ACAAGCCTGTCCTGTAGAGT AGGATTTGAACCTACGGCAC 2818 0.333 52.3
rpl20-acpP_p2 rpl20-acpP GCACGCTTTCAAAGGTCATC AGGATTTGAACCTACGGCAC 2619 0.333 52.2
rpl20-acpP_p3 rpl20-acpP CCTGTCCTGTAGAGTGGGAA AGGATTTGAACCTACGGCAC 2813 0.333 52.0
rpl20-acpP_p4 rpl20-acpP GAAACGTAGCACGAAAACGG AGGATTTGAACCTACGGCAC 2474 0.333 51.9
rpl20-acpP_p5 rpl20-acpP GGAAACGTAGCACGAAAACG AGGATTTGAACCTACGGCAC 2475 0.333 51.9
rns-trnI(gau)_p1 rns-trnI(gau) GTAACCGTACTGGAAGGTGC ATTTGAACCAGAGACCTCGC 162–175 1.000 88.9
rns-trnI(gau)_p2 rns-trnI(gau) AGGTAACCGTACTGGAAGGT ATTTGAACCAGAGACCTCGC 164–177 1.000 88.7
rns-trnI(gau)_p3 rns-trnI(gau) GTAACCGTACTGGAAGGTGC CTGGGCCATTCTGGATTTGA 176–189 1.000 88.6
rns-trnI(gau)_p4 rns-trnI(gau) AGGTAACCGTACTGGAAGGT CTGGGCCATTCTGGATTTGA 178–191 1.000 88.3
rns-trnI(gau)_p5 rns-trnI(gau) GGTAACCGTACTGGAAGGTG ATTTGAACCAGAGACCTCGC 163–176 1.000 88.2
rrn5_p1 rrn5 ATCTCCCCCAAGAGTTCACA GTAGCTGCACACGGTTACTT 1357–1655 0.667 76.6
rrn5_p2 rrn5 TCTCCCCCAAGAGTTCACAT GTAGCTGCACACGGTTACTT 1356–1654 0.667 76.6
rrn5_p3 rrn5 TAGTAAACGGAACCACGCTG GTAGCTGCACACGGTTACTT 852–1150 0.667 76.5
rrn5_p4 rrn5 GTAGTAAACGGAACCACGCT GTAGCTGCACACGGTTACTT 853–1151 0.667 76.4
rrn5_p5 rrn5 TTCGGTCCATATCCGGTGTA GTAGCTGCACACGGTTACTT 1212–1510 0.667 76.4
syfB_p1 syfB TTTAATAAGGGCGAGCGACC CTTTGACTCCGCCATTCGTA 2996 0.333 52.8
syfB_p2 syfB TTTAATAAGGGCGAGCGACC TTTGACTCCGCCATTCGTAG 2995 0.333 52.8
syfB_p3 syfB TTTAATAAGGGCGAGCGACC AAGACGGTAGCACAGGTACT 2831 0.333 52.3
syfB_p4 syfB TTTAATAAGGGCGAGCGACC CAAAAGACGGTAGCACAGGT 2834 0.333 51.9
syfB_p5 syfB TTTAATAAGGGCGAGCGACC GGTCAAAAGACGGTAGCACA 2837 0.333 51.9

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
Coscinodiscus granii NC_059930.1 123615 View on NCBI ↗
Coscinodiscus radiatus NC_024081.1 122213 View on NCBI ↗
Coscinodiscus wailesii NC_059929.1 122056 View on NCBI ↗