Markers + reference

Codium

4 species · Codiaceae · Bryopsidales

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Species 4
Genome length 79–92 kb
Candidate markers 217
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 217 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rns-trnN Genome 541 0.3920 0.00 57.4 yes View details
ftsH Genome 3930 0.2624 0.00 52.3 yes View details
rpoC2 Genome 3705 0.2203 0.98 77.3 yes View details
psbA-rbcL Genome 675 0.3709 0.93 80.8 no View details
rbcL Genome 3149 0.1902 0.97 79.2 yes View details
orf276 Genome 831 0.2964 0.97 84.1 yes View details
rps19 Genome 813 0.1233 0.97 83.7 yes View details
ycf3 Genome 848 0.1875 0.99 83.6 yes View details
rpl5 Genome 827 0.1949 0.96 83.6 yes View details
orf107-petG Genome 1360 0.1324 0.94 83.0 yes View details
atpF Genome 875 0.1920 0.98 82.8 yes View details
rps2 Genome 690 0.1583 0.96 82.5 yes View details
ccs1 Genome 1142 0.1990 0.98 82.3 yes View details
psbB Genome 2331 0.1523 0.97 82.2 yes View details
accD Genome 1026 0.1625 0.96 81.7 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
rns-trnN_p1 rns-trnN AGAGCTAGTGACTCAAGCGA CTCTACCATTGAGCTACTAAGGA 517–743 1.000 55.6
rns-trnN_p2 rns-trnN GTAACCGTACTGGAAGGTGC CTCTACCATTGAGCTACTAAGGA 485–711 1.000 54.8
rns-trnN_p3 rns-trnN AGGTAACCGTACTGGAAGGT CTCTACCATTGAGCTACTAAGGA 487–713 1.000 54.5
rns-trnN_p4 rns-trnN AGAGCTAGTGACTCAAGCGA TCTACCATTGAGCTACTAAGGA 516–742 1.000 54.3
rns-trnN_p5 rns-trnN GCTAGTGACTCAAGCGAAGT CTCTACCATTGAGCTACTAAGGA 514–740 1.000 54.2
ftsH_p1 ftsH AGTATTTACATAGGCTTCTTCG ACACAAAATGTTGGCCTGAC 703 0.250 10.0
ftsH_p2 ftsH AGTATTTACATAGGCTTCTTCG GACACAAAATGTTGGCCTGA 704 0.250 10.0
ftsH_p3 ftsH AGTATTTACATAGGCTTCTTCG AGACACAAAATGTTGGCCTG 705 0.250 10.0
ftsH_p4 ftsH AGTATTTACATAGGCTTCTTCG CACAAAATGTTGGCCTGACT 702 0.250 10.0
ftsH_p5 ftsH AGTATTTACATAGGCTTCTTCG GACACAAAATGTTGGCCTGAC 704 0.250 10.0
ycf3_p1 ycf3 GGGAAAATTTTACCACGCCG AAAACAATCCAGTCGGCCTT 1145 0.250 49.8
ycf3_p2 ycf3 GGGAAAATTTTACCACGCCG AAACAATCCAGTCGGCCTTT 1144 0.250 49.8
ycf3_p3 ycf3 GGGAAAATTTTACCACGCCG TCCAGTCGGCCTTTCTTCTA 1138 0.250 49.3
ycf3_p4 ycf3 GGGAAAATTTTACCACGCCG CCCTTCATCGTCTTTGAGCA 1254 0.250 49.1
ycf3_p5 ycf3 GGGAAAATTTTACCACGCCG TTTTCGCAGTTTAACACGCC 1272 0.250 49.0
rpoC2_p1 rpoC2 TGCCTTCCATACTAAGCAAGG TGGAACAATTTGGATCGCCA 1291 0.250 39.1
rpoC2_p2 rpoC2 TGCCTTCCATACTAAGCAAGG ATCGCCAAAGTGTTTGCATC 1278 0.250 36.9
rpoC2_p3 rpoC2 TGCCTTCCATACTAAGCAAGG GATCGCCAAAGTGTTTGCAT 1279 0.250 36.9
rpoC2_p4 rpoC2 GCCTTCCATACTAAGCAAGGA TGGAACAATTTGGATCGCCA 1290 0.250 36.8
rpoC2_p5 rpoC2 TGGAGTTGTGGAGTCAGAAA TGGAACAATTTGGATCGCCA 867 0.250 35.8
ccs1_p1 ccs1 GCTTTTTCACGAACAGAGGC TGGATCTAATGCCCCAAACG 2250 0.250 49.3
ccs1_p2 ccs1 GCTTTTTCACGAACAGAGGC GATCTAATGCCCCAAACGGT 2248 0.250 49.3
ccs1_p3 ccs1 GCTTTTTCACGAACAGAGGC CGGCTTTTTCAAAACCAGCA 1918 0.250 49.2
ccs1_p4 ccs1 GCTTTTTCACGAACAGAGGC TCAATCGCTAATGCTCGGAC 2204 0.250 48.5
ccs1_p5 ccs1 GCTTTTTCACGAACAGAGGC GCCCCAAACGGTTCATCTAA 2240 0.250 48.3
psbB_p1 psbB TGTCCATAGAGTGCTTGTGT GCCTGGAGTGACTTTTCCAT 2940 0.250 36.2
psbB_p2 psbB TGTCCATAGAGTGCTTGTGT AAAAGTGTAGTTCCCCAGCC 2957 0.250 35.5
psbB_p3 psbB TGTCCATAGAGTGCTTGTGTT GCCTGGAGTGACTTTTCCAT 2940 0.250 34.2
psbB_p4 psbB TTGTCCATAGAGTGCTTGTGT GCCTGGAGTGACTTTTCCAT 2941 0.250 34.2
psbB_p5 psbB TGTCCATAGAGTGCTTGTGT CAGCCTGGAGTGACTTTTCC 2942 0.250 34.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Codium arabicum NC_039524.1 79309 View on NCBI ↗
Codium arenicola NC_037366.1 83933 View on NCBI ↗
Codium fragile MN853876.1 83788 View on NCBI ↗
Codium simulans NC_032043.1 91509 View on NCBI ↗