Markers + reference

Skeletonema

5 species · Skeletonemataceae · Thalassiosirales

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Species 5
Genome length 127–127 kb
Candidate markers 355
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 355 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petF Genome 300 0.1422 1.00 73.7 yes View details
ycf89-rns Genome 274 0.1682 1.00 78.7 yes View details
dnaK Genome 1797 0.0634 1.00 78.1 yes View details
thiG Genome 810 0.0881 1.00 78.7 yes View details
rns-ycf89 Genome 274 0.1672 1.00 78.6 yes View details
ycf33-trnT(ugu) Genome 280 0.2331 1.00 77.5 yes View details
chlI-petA Genome 381 0.2340 0.99 78.9 yes View details
rps20-rpoB Genome 445 0.1572 0.99 80.9 yes View details
ycf45 Genome 1365 0.0812 1.00 79.5 yes View details
trnV(uac)-psbH Genome 217 0.1594 0.91 79.3 yes View details
petN-trnD(guc) Genome 189 0.0612 1.00 83.9 yes View details
trnQ(uug)-trnR(acg) Genome 67 0.1468 1.00 83.3 yes View details
tufA Genome 1230 0.0565 1.00 80.3 yes View details
trnG(gcc)-psbZ Genome 148 0.1160 0.99 79.9 yes View details
dnaK-rpl3 Genome 353 0.1434 0.99 79.5 yes View details
ycf46 Genome 1494 0.0681 1.00 79.4 yes View details
rpl2 Genome 828 0.0662 1.00 79.3 yes View details
rps3 Genome 645 0.0546 1.00 79.3 yes View details
ycf46 Genome 1494 0.0681 1.00 79.2 yes View details
psaF-psbI Genome 228 0.0880 1.00 79.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petF_p1 petF TCCTATGGAACGTCACTGGT CGTTGGAGAGACAAACCAGT 1215–1235 1.000 89.4
petF_p2 petF TCCTATGGAACGTCACTGGT TTTGGGCACATGAACGTACA 1253–1273 0.800 82.4
petF_p3 petF TGGACATGGGTTCAATTCCC TTTGGGCACATGAACGTACA 1333–1353 0.800 80.9
petF_p4 petF TACGTGGAAAAGCAAGTCGT TTTGGGCACATGAACGTACA 809–827 0.600 73.2
petF_p5 petF TCCTATGGAACGTCACTGGT GGTGGAAATCCGGGTCAATT 1502 0.200 46.2
ycf89-rns_p1 ycf89-rns TTGGTATTCAGAACGCCCAG TCTCGTACGACTTGCATGTG 517–527 0.600 71.0
ycf89-rns_p2 ycf89-rns TTGGTATTCAGAACGCCCAG CATTGCGGAAAATTCCCCAC 799–809 0.600 70.5
ycf89-rns_p3 ycf89-rns TTGGTATTCAGAACGCCCAG TATTGCTCCGTCAGGCTTTC 822–832 0.600 70.2
ycf89-rns_p4 ycf89-rns TTGGTATTCAGAACGCCCAG CAACCCATAGGCAGTCTTCC 851–861 0.600 69.8
ycf89-rns_p5 ycf89-rns TTGGTATTCAGAACGCCCAG AGCAGTCGTTTCCAACTGTT 599 0.200 46.8
ycf46_p1 ycf46 TGGAGAAGTTATGGGCAACG GGGTGCTATTCGACCAATCA 2407 0.200 44.5
ycf46_p2 ycf46 TGGAGAAGTTATGGGCAACG TGGGTGCTATTCGACCAATC 2408 0.200 44.5
ycf46_p3 ycf46 CGTGATGCTGTAGGTTGGAG GGGTGCTATTCGACCAATCA 2422 0.200 42.6
ycf46_p4 ycf46 CGTGATGCTGTAGGTTGGAG TGGGTGCTATTCGACCAATC 2423 0.200 42.6
ycf46_p5 ycf46 GGAGAAGTTATGGGCAACGA GGGTGCTATTCGACCAATCA 2406 0.200 42.2
trnQ(uug)-trnR(acg)_p1 trnQ(uug)-trnR(acg) GAGTCAAAGTCCACAGCCTT GGGGTTCGAATCCCTTCTTG 129–141 1.000 87.9
trnQ(uug)-trnR(acg)_p2 trnQ(uug)-trnR(acg) CAAAGTCCACAGCCTTACCA GGGGTTCGAATCCCTTCTTG 125–137 1.000 87.8
trnQ(uug)-trnR(acg)_p3 trnQ(uug)-trnR(acg) AAAGTCCACAGCCTTACCAC GGGGTTCGAATCCCTTCTTG 124–136 1.000 87.8
trnQ(uug)-trnR(acg)_p4 trnQ(uug)-trnR(acg) GTGGCAGGATTCGAACCTAC GGGGTTCGAATCCCTTCTTG 157–169 1.000 87.2
trnQ(uug)-trnR(acg)_p5 trnQ(uug)-trnR(acg) GTCCACAGCCTTACCACTTG GGGGTTCGAATCCCTTCTTG 121–133 1.000 86.2
dnaK_p1 dnaK TATTTCGCGTGCAATTGTCG CATTGGGCCTCTTGCAAAAC 2998 0.200 45.2
dnaK_p2 dnaK GGGATTGCTGTTATCCGTGT GTGTAACGATACAAGGCCCA 2917 0.200 44.6
dnaK_p3 dnaK GGGATTGCTGTTATCCGTGT TGTGTAACGATACAAGGCCC 2918 0.200 44.6
dnaK_p4 dnaK TATTTCGCGTGCAATTGTCG ATTGGGCCTCTTGCAAAACT 2997 0.200 44.5
dnaK_p5 dnaK TATTTCGCGTGCAATTGTCG TCATTGGGCCTCTTGCAAAA 2999 0.200 44.5
dnaK-rpl3_p1 dnaK-rpl3 TCCAGCATCAACAGTTGCTT GTTACCAAGTTGACCTGCCA 1295–1309 0.600 72.8
dnaK-rpl3_p2 dnaK-rpl3 TCCAGCATCAACAGTTGCTT TGTTACCAAGTTGACCTGCC 1296–1310 0.600 72.8
dnaK-rpl3_p3 dnaK-rpl3 CCAGCATCAACAGTTGCTTG GTTACCAAGTTGACCTGCCA 1294–1308 0.600 72.4
dnaK-rpl3_p4 dnaK-rpl3 TCCAGCATCAACAGTTGCTT CAGGTTTTCCAGGAACAGCT 1386 0.200 47.8
dnaK-rpl3_p5 dnaK-rpl3 CCAGCATCAACAGTTGCTTG CAGGTTTTCCAGGAACAGCT 1385 0.200 47.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Skeletonema costatum NC_058703.1 127351 View on NCBI ↗
Skeletonema grevillei NC_058705.1 126883 View on NCBI ↗
Skeletonema marinoi NC_058701.1 127212 View on NCBI ↗
Skeletonema pseudocostatum NC_058704.1 127011 View on NCBI ↗
Skeletonema tropicum NC_058702.1 127112 View on NCBI ↗