Markers + reference

Conticribra

2 species · Thalassiosiraceae · Thalassiosirales

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Species 2
Genome length 128–129 kb
Candidate markers 356
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 356 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaB-petF Genome 1182 0.2863 0.22 64.7 yes View details
rpoB-rps20 Genome 488 0.2729 0.87 79.6 yes View details
ycf90 Genome 1422 0.2124 1.00 79.7 yes View details
trnP-UGG-ycf89 Genome 350 0.2663 0.97 77.5 yes View details
ycf89 Genome 963 0.1838 1.00 78.8 no View details
dnaK Genome 1848 0.1512 1.00 78.3 yes View details
clpC Genome 2673 0.2541 0.98 78.0 yes View details
ycf89 Genome 963 0.1838 1.00 78.8 yes View details
trnS-GCU-trnD-GUC Genome 73 0.3000 0.96 82.3 yes View details
dnaK-rpl3 Genome 322 0.2476 0.95 81.2 yes View details
bas1 Genome 636 0.1006 1.00 80.5 yes View details
rpl6 Genome 543 0.1289 1.00 80.4 yes View details
rps3 Genome 648 0.1862 0.99 80.3 yes View details
rpl2 Genome 828 0.1280 1.00 79.8 yes View details
rpoA Genome 963 0.1020 1.00 79.5 yes View details
sufC Genome 756 0.1164 1.00 79.4 yes View details
sufB Genome 1458 0.1118 1.00 79.3 yes View details
ycf39 Genome 990 0.1656 0.99 79.3 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psaB-petF_p1 psaB-petF GAGCTTTAGATGCACGTGGA AGATGCAGCAGAAGAAGCAG 1995 0.500 57.8
psaB-petF_p2 psaB-petF AGGAGCTTTAGATGCACGTG AGATGCAGCAGAAGAAGCAG 1997 0.500 57.8
psaB-petF_p3 psaB-petF GGCACATGAACGTACTCCAT AGATGCAGCAGAAGAAGCAG 1565 0.500 57.7
psaB-petF_p4 psaB-petF AAAAATCGGCCCAGGTGATT AGATGCAGCAGAAGAAGCAG 2075 0.500 57.4
psaB-petF_p5 psaB-petF AAAATCGGCCCAGGTGATTT AGATGCAGCAGAAGAAGCAG 2074 0.500 57.4
sufB_p1 sufB TTACTGTGTACGCAGCATCC CAATTGGATCGACTTCGGGT 2223 0.500 59.8
sufB_p2 sufB TTACTGTGTACGCAGCATCC CCAAATGCGAACGTTGTTCA 2103 0.500 59.1
sufB_p3 sufB CGTTTGGCACTGGATCTACA CAATTGGATCGACTTCGGGT 2406 0.500 59.1
sufB_p4 sufB TTTGGCACTGGATCTACACG CAATTGGATCGACTTCGGGT 2404 0.500 59.1
sufB_p5 sufB TTACTGTGTACGCAGCATCC CACCCGAAAACCCTTCGTTA 2313 0.500 59.0
sufC_p1 sufC ACTCGAAGTCGCATTGTCTC GCCTCCGCTAAGAATGTGAA 1320 0.500 59.7
sufC_p2 sufC CTCGAAGTCGCATTGTCTCA GCCTCCGCTAAGAATGTGAA 1319 0.500 59.7
sufC_p3 sufC CTTATGCGCAGGGGATTCTT GCCTCCGCTAAGAATGTGAA 1507 0.500 59.6
sufC_p4 sufC TTATGCGCAGGGGATTCTTC GCCTCCGCTAAGAATGTGAA 1506 0.500 59.5
sufC_p5 sufC GCGCAGGGGATTCTTCTAAA GCCTCCGCTAAGAATGTGAA 1502 0.500 59.5
bas1_p1 bas1 CAAGCAGAAGGTCACAGGTT TAAGGCTGCTTTTCGGGTTT 1255 0.500 59.7
bas1_p2 bas1 CAAGCAGAAGGTCACAGGTT TTAAGGCTGCTTTTCGGGTT 1256 0.500 59.7
bas1_p3 bas1 CAAGCAGAAGGTCACAGGTT TTTAAGGCTGCTTTTCGGGT 1257 0.500 59.7
bas1_p4 bas1 GCAGAAGGTCACAGGTTCAA TAAGGCTGCTTTTCGGGTTT 1252 0.500 59.7
bas1_p5 bas1 GCAGAAGGTCACAGGTTCAA TTAAGGCTGCTTTTCGGGTT 1253 0.500 59.7
rpoB-rps20_p1 rpoB-rps20 AGGAATAACCAGTTGTGCCG AGAAACACCAGCAGAACGTT 1321 0.500 58.3
rpoB-rps20_p2 rpoB-rps20 GGAATAACCAGTTGTGCCGA AGAAACACCAGCAGAACGTT 1320 0.500 58.2
rpoB-rps20_p3 rpoB-rps20 TGCCGAGTAATTTGCGGTAT AGAAACACCAGCAGAACGTT 1306 0.500 57.1
rpoB-rps20_p4 rpoB-rps20 GTTGTGCCGAGTAATTTGCG AGAAACACCAGCAGAACGTT 1310 0.500 56.5
rpoB-rps20_p5 rpoB-rps20 ACCAGTTGTGCCGAGTAATT AGAAACACCAGCAGAACGTT 1314 0.500 55.2
trnS-GCU-trnD-GUC_p1 trnS-GCU-trnD-GUC AATGGCTGAGTGGTCGAAAG AGACTCGAACTCGCAACTTC 217–218 1.000 86.9
trnS-GCU-trnD-GUC_p2 trnS-GCU-trnD-GUC AATGGCTGAGTGGTCGAAAG GAGACTCGAACTCGCAACTT 218–219 1.000 86.9
trnS-GCU-trnD-GUC_p3 trnS-GCU-trnD-GUC GAAATGGCTGAGTGGTCGAA AGACTCGAACTCGCAACTTC 219–220 1.000 86.8
trnS-GCU-trnD-GUC_p4 trnS-GCU-trnD-GUC GAAATGGCTGAGTGGTCGAA GAGACTCGAACTCGCAACTT 220–221 1.000 86.7
trnS-GCU-trnD-GUC_p5 trnS-GCU-trnD-GUC GGAGAAATGGCTGAGTGGTC AGACTCGAACTCGCAACTTC 222–223 1.000 86.2

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
Conticribra guillardii PV423721.1 129219 View on NCBI ↗
Conticribra weissflogii NC_025314.1 127601 View on NCBI ↗