Markers + reference

Porosira

2 species · Thalassiosiraceae · Thalassiosirales

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Species 2
Genome length 127–131 kb
Candidate markers 356
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 356 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-rps20 Genome 1022 0.2606 0.55 73.5 yes View details
trnT-UGU-ycf33 Genome 277 0.2819 0.82 74.1 yes View details
rps16 Genome 234 0.3376 1.00 72.5 yes View details
dnaK Genome 1809 0.2127 0.99 79.0 yes View details
clpC Genome 2706 0.2316 0.99 78.0 yes View details
thiG Genome 807 0.1174 0.99 80.5 yes View details
rns-trnI-GAU Genome 56 0.1250 1.00 84.0 yes View details
trnI-GAU-rns Genome 56 0.1250 1.00 84.0 yes View details
rpl3 Genome 657 0.1635 0.95 83.8 yes View details
rps2 Genome 726 0.2075 0.96 83.2 yes View details
trnR-UCU-psaE Genome 178 0.3394 0.93 81.0 yes View details
trnP-UGG-psaA Genome 250 0.2213 0.94 80.6 no View details
rps9 Genome 453 0.1300 0.93 80.4 yes View details
rpl4 Genome 648 0.1745 0.99 79.7 yes View details
sufC Genome 762 0.1204 0.99 79.5 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
sufC_p1 sufC AAATGAGAAAGGTCAGGGCG GCCTCCGCTAAGAATGTGAA 1563 0.500 58.4
sufC_p2 sufC AAATGAGAAAGGTCAGGGCG TGCAAACTCTCCCTCTGGTA 1891 0.500 58.4
sufC_p3 sufC AAATGAGAAAGGTCAGGGCG GAATCCGATCAGCTTCACGT 1697 0.500 58.0
sufC_p4 sufC AAATGAGAAAGGTCAGGGCG ATGCACTAAGAAACCGGCAA 1612 0.500 57.8
sufC_p5 sufC AAATGAGAAAGGTCAGGGCG TGCACTAAGAAACCGGCAAT 1611 0.500 57.8
trnR-UCU-psaE_p1 trnR-UCU-psaE TTCGATTCCTACTGGGCCTA ACGAACTTTTGAATTACGATCA 216–225 1.000 52.0
trnR-UCU-psaE_p2 trnR-UCU-psaE AACGGATAGGACAGGAACCT ACGAACTTTTGAATTACGATCA 264 0.500 20.0
trnR-UCU-psaE_p3 trnR-UCU-psaE ACGGATAGGACAGGAACCTT ACGAACTTTTGAATTACGATCA 263 0.500 20.0
trnR-UCU-psaE_p4 trnR-UCU-psaE AACGGATAGGACAGGAACCT ACGAACTTTTGAATTACGATCAA 264 0.500 20.0
trnR-UCU-psaE_p5 trnR-UCU-psaE ACGGATAGGACAGGAACCTT ACGAACTTTTGAATTACGATCAA 263 0.500 20.0
rps2_p1 rps2 AACAAAATCGCCCTTCTGGT CACCATTACTACCACGCGAA 1797 0.500 60.0
rps2_p2 rps2 AACAAAATCGCCCTTCTGGT ACCCAAGCTTTGAATTCCGT 2118 0.500 59.9
rps2_p3 rps2 CTCCAGTTGCAGCTGAAGAA CACCATTACTACCACGCGAA 1497 0.500 59.1
rps2_p4 rps2 TCCAGTTGCAGCTGAAGAAG CACCATTACTACCACGCGAA 1496 0.500 59.1
rps2_p5 rps2 TCCAGTTGCAGCTGAAGAAG ACCCAAGCTTTGAATTCCGT 1817 0.500 59.1
rpoB-rps20_p1 rpoB-rps20 TCACTGGGAATTACGCGTTT CTGCTCAACTAAAAGCTGCG 1491 0.500 56.7
rpoB-rps20_p2 rpoB-rps20 TTCACTGGGAATTACGCGTT CTGCTCAACTAAAAGCTGCG 1492 0.500 56.7
rpoB-rps20_p3 rpoB-rps20 TTTCACTGGGAATTACGCGT CTGCTCAACTAAAAGCTGCG 1493 0.500 56.7
rpoB-rps20_p4 rpoB-rps20 GGTTGTCCATCCCAATTCCA CTGCTCAACTAAAAGCTGCG 1653 0.500 56.3
rpoB-rps20_p5 rpoB-rps20 TGGTTGTCCATCCCAATTCC CTGCTCAACTAAAAGCTGCG 1654 0.500 56.3
trnT-UGU-ycf33_p1 trnT-UGU-ycf33 TGGTGTAGCTCAACGGTAGA CGACCTTGGGCTTATGAGTC 707–735 1.000 90.8
trnT-UGU-ycf33_p2 trnT-UGU-ycf33 GATTCCGGGTTTTCAGGGTT CGACCTTGGGCTTATGAGTC 1154 0.500 58.9
trnT-UGU-ycf33_p3 trnT-UGU-ycf33 TTGATTCCGGGTTTTCAGGG CGACCTTGGGCTTATGAGTC 1156 0.500 58.9
trnT-UGU-ycf33_p4 trnT-UGU-ycf33 GGCGATTCCCTAATTCTGGG CGACCTTGGGCTTATGAGTC 1318 0.500 58.7
trnT-UGU-ycf33_p5 trnT-UGU-ycf33 GATTCCGGGTTTTCAGGGTT TAGTAGATGGCTCTGGTGGG 1185 0.500 58.6
rns-trnI-GAU_p1 rns-trnI-GAU GACTGGGGTGAAGTCGTAAC CTGGGCCATTCTGGATTTGA 192 1.000 81.1
rns-trnI-GAU_p2 rns-trnI-GAU GGAGGGTGCCTAAGGTAGAA CTGGGCCATTCTGGATTTGA 217 1.000 80.4
rns-trnI-GAU_p3 rns-trnI-GAU GGGGTGAAGTCGTAACAAGG CTGGGCCATTCTGGATTTGA 188 1.000 80.2
rns-trnI-GAU_p4 rns-trnI-GAU GTAACCGTACTGGAAGGTGC CTGGGCCATTCTGGATTTGA 169 1.000 79.9
rns-trnI-GAU_p5 rns-trnI-GAU TGACTGGGGTGAAGTCGTAA CTGGGCCATTCTGGATTTGA 193 1.000 79.4

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
Porosira glacialis PV423733.1 131464 View on NCBI ↗
Porosira pentaportula PV423677.1 126651 View on NCBI ↗