Markers + reference

Cyclotella

6 species · Stephanodiscaceae · Stephanodiscales

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Species 6
Genome length 127–134 kb
Candidate markers 354
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 354 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-psaC Genome 801 0.3343 0.87 80.0 yes View details
ccsA Genome 1056 0.3020 0.94 82.0 yes View details
thiS-trnQ-UUG Genome 863 0.3334 0.50 72.5 yes View details
dnaK Genome 1788 0.1584 0.99 81.2 yes View details
rpl13-rps9 Genome 363 0.4454 0.53 68.0 yes View details
clpC Genome 3195 0.2425 0.91 78.0 yes View details
ccsA Genome 1056 0.2520 0.94 80.1 no View details
psaC-psbA Genome 801 0.3461 0.84 79.3 yes View details
rpl6 Genome 600 0.1756 0.99 84.5 yes View details
rpl4 Genome 654 0.2016 0.95 83.2 yes View details
trnK-UUU-ycf12 Genome 172 0.1167 1.00 82.7 yes View details
rpl5 Genome 723 0.1062 0.96 82.7 yes View details
atpD Genome 567 0.2063 0.96 82.3 yes View details
rps3 Genome 711 0.1234 0.92 82.0 yes View details
rpl3 Genome 681 0.1079 0.97 81.6 yes View details
rpl13 Genome 489 0.2003 0.99 81.2 yes View details
atpA Genome 1515 0.1277 0.98 80.3 yes View details
ycf90 Genome 1371 0.1488 1.00 80.3 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
atpA_p1 atpA ATACTCCAACCACCCCAAGA TGCACGGGCTTTATACGATT 2521–2538 0.333 60.9
atpA_p2 atpA CTCCAACCACCCCAAGAATC TGCACGGGCTTTATACGATT 2518–2535 0.333 60.0
atpA_p3 atpA TACTCCAACCACCCCAAGAA TGCACGGGCTTTATACGATT 2520–2537 0.333 59.9
atpA_p4 atpA ATACCTTGACGCCACATTGG TGCACGGGCTTTATACGATT 2461–2478 0.333 59.4
atpA_p5 atpA AACCCAATGCCAAATTGCTG TGCACGGGCTTTATACGATT 2647 0.167 42.6
atpD_p1 atpD AAGCCTTCACCTACAGGGAT AATAGAGCAATCGCGACGTT 1105 0.167 45.8
atpD_p2 atpD AAGCCTTCACCTACAGGGAT ATAGAGCAATCGCGACGTTT 1104 0.167 45.8
atpD_p3 atpD AGCCTTCACCTACAGGGATT AATAGAGCAATCGCGACGTT 1104 0.167 45.8
atpD_p4 atpD AGCCTTCACCTACAGGGATT ATAGAGCAATCGCGACGTTT 1103 0.167 45.8
atpD_p5 atpD CATCAAGCCCATAAACCCGA ATAGAGCAATCGCGACGTTT 932 0.167 45.6
trnK-UUU-ycf12_p1 trnK-UUU-ycf12 TCGAACCCAGAACAAATCGG AGCTGACCTATAACTTGCCA 301–331 1.000 76.3
trnK-UUU-ycf12_p2 trnK-UUU-ycf12 GGACTCGAACCCAGAACAAA AGCTGACCTATAACTTGCCA 305–335 1.000 75.8
trnK-UUU-ycf12_p3 trnK-UUU-ycf12 TCGAACCCAGAACAAATCGG AGCTGACCTATAACTTGCCAA 301–331 1.000 74.4
trnK-UUU-ycf12_p4 trnK-UUU-ycf12 GGACTCGAACCCAGAACAAA AGCTGACCTATAACTTGCCAA 305–335 1.000 74.0
trnK-UUU-ycf12_p5 trnK-UUU-ycf12 CGAACCCAGAACAAATCGGT AGCTGACCTATAACTTGCCA 300–330 1.000 74.0
ycf90_p1 ycf90 TGTTGTATTGGGCTTGCTGT ACGCAAGATCGTCAACAAGT 2560–2576 0.333 56.6
ycf90_p2 ycf90 TGTTGTATTGGGCTTGCTGT GTTTTTGGAACACCACGTCC 2593–2609 0.333 56.1
ycf90_p3 ycf90 TGTTGTATTGGGCTTGCTGT TTTTTGGAACACCACGTCCT 2608 0.167 45.6
ycf90_p4 ycf90 AACTTGCCAAAGGTATGGGG TTTTTGGAACACCACGTCCT 2706 0.167 45.1
ycf90_p5 ycf90 AACTTGCCAAAGGTATGGGG ACGCAAGATCGTCAACAAGT 2674 0.167 45.1
psbA-psaC_p1 psbA-psaC TCGTAGCTGCACATGGTTAC TGAGCCTGATACACGAAACG 1857 0.167 46.6
psbA-psaC_p2 psbA-psaC CGTAGCTGCACATGGTTACT TGAGCCTGATACACGAAACG 1856 0.167 46.5
psbA-psaC_p3 psbA-psaC TGCATCTTACATGGGTCGTG TGAGCCTGATACACGAAACG 2231 0.167 46.4
psbA-psaC_p4 psbA-psaC TCGTAGCTGCACATGGTTAC TTGGGATGGATGTAAAGCCG 1299 0.167 46.2
psbA-psaC_p5 psbA-psaC CGTAGCTGCACATGGTTACT TTGGGATGGATGTAAAGCCG 1298 0.167 46.2
ccsA_p1 ccsA CGAGTTGTTTCAGCCCCTAA TCTGCTGTTCGTCGAGAAAC 1541–1583 0.333 56.9
ccsA_p2 ccsA CGGCTTTACATCCATCCCAA CTGCTGTTCGTCGAGAAACT 1467 0.167 44.4
ccsA_p3 ccsA CGGCTTTACATCCATCCCAA GTCTGCTGTTCGTCGAGAAA 1469 0.167 44.4
ccsA_p4 ccsA CGGCTTTACATCCATCCCAA TCTGCTGTTCGTCGAGAAAC 1468 0.167 44.4
ccsA_p5 ccsA CGAGTTGTTTCAGCCCCTAA CTGCTGTTCGTCGAGAAACT 1582 0.167 43.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Cyclotella aff. atomus PV356815.1 133867 View on NCBI ↗
Cyclotella atomus PV423670.1 133026 View on NCBI ↗
Cyclotella baltica PV423678.1 129664 View on NCBI ↗
Cyclotella cf. meneghiniana PV423718.1 132587 View on NCBI ↗
Cyclotella distinguenda PV423719.1 127168 View on NCBI ↗
Cyclotella stylorum PV423705.1 129353 View on NCBI ↗