Markers + reference

Tetradesmus

5 species · Scenedesmaceae · Sphaeropleales

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Species 5
Genome length 152–175 kb
Candidate markers 228
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 228 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA Genome 2731 0.3032 0.93 75.4 yes View details
psbA-V9305_pgt009 Genome 1660 0.2992 0.97 87.8 yes View details
V9305_pgt009-V9305_pgr006 Genome 1440 0.2360 0.94 79.2 yes View details
V9305_pgt028-V9305_pgt029 Genome 769 0.3823 0.66 74.5 yes View details
psaB-V9305_pgt022 Genome 1289 0.1993 0.99 88.7 yes View details
psbM-psbZ Genome 800 0.2068 0.99 87.8 yes View details
V9305_pgt014-V9305_pgt015 Genome 544 0.2210 0.99 87.5 yes View details
psbJ-psaA Genome 965 0.1535 0.99 85.6 yes View details
psbC-atpF Genome 633 0.1737 0.99 85.2 yes View details
rpl20-rbcL Genome 677 0.2026 1.00 84.7 yes View details
rpoBb-rpoBa Genome 648 0.2573 0.99 84.6 yes View details
psbL-V9305_pgt002 Genome 746 0.1485 0.99 84.5 yes View details
atpB-V9305_pgt019 Genome 775 0.2195 0.98 84.3 yes View details
rpoC2-rps3 Genome 633 0.2591 0.99 84.2 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbC-atpF_p1 psbC-atpF GAGCTACGTGTGCACCTAAA CAAGAAGCAAGCCAAAGAGC 1117–1320 0.800 81.1
psbC-atpF_p2 psbC-atpF GAGCTACGTGTGCACCTAAA AGGTGTATTCCGAGCAACAC 1016–1219 0.800 81.0
psbC-atpF_p3 psbC-atpF ACAATCCAACCATCACCACC CAAGAAGCAAGCCAAAGAGC 1625–1828 0.800 80.4
psbC-atpF_p4 psbC-atpF CAATCCAACCATCACCACCA CAAGAAGCAAGCCAAAGAGC 1624–1827 0.800 80.4
psbC-atpF_p5 psbC-atpF GGTAAACACCCCCAAAACCT CAAGAAGCAAGCCAAAGAGC 1345–1548 0.600 72.6
rpoC2-rps3_p1 rpoC2-rps3 CGTTGCATACGTTCTACTCCT ATTGCACGTTCAGAATGGGT 1466–1478 0.400 49.6
rpoC2-rps3_p2 rpoC2-rps3 CGTTGCATACGTTCTACTCCT GCAGGTCGTGTTCCTTTACA 1442–1454 0.400 49.4
rpoC2-rps3_p3 rpoC2-rps3 ACTTTTGCCCTTCTTGACTCA ATTGCACGTTCAGAATGGGT 1004–1016 0.400 49.1
rpoC2-rps3_p4 rpoC2-rps3 CGTTGCATACGTTCTACTCCT GTGCAGGTCGTGTTCCTTTA 1444 0.200 37.8
rpoC2-rps3_p5 rpoC2-rps3 CGTTGCATACGTTCTACTCCT TGCAGGTCGTGTTCCTTTAC 1443 0.200 37.8
rpoBb-rpoBa_p1 rpoBb-rpoBa ACCATTGGACGCTGAACAAT GGAGGTGTGTCACGTGATAC 1553–1570 0.400 58.5
rpoBb-rpoBa_p2 rpoBb-rpoBa ACCATTGGACGCTGAACAAT TTGCGTTAATGGGGGTTTCA 1204 0.200 47.3
rpoBb-rpoBa_p3 rpoBb-rpoBa ACCATTGGACGCTGAACAAT AAACTTGCGTTAATGGGGGT 1208 0.200 47.2
rpoBb-rpoBa_p4 rpoBb-rpoBa ACCATTGGACGCTGAACAAT AACTTGCGTTAATGGGGGTT 1207 0.200 47.2
rpoBb-rpoBa_p5 rpoBb-rpoBa ACCATTGGACGCTGAACAAT ACTTGCGTTAATGGGGGTTT 1206 0.200 47.2
psbL-V9305_pgt002_p1 psbL-V9305_pgt002 TTCACGCATTAGCAGTTCCT GGACTTGAACCCTCACGATC 1429–1831 1.000 88.1
psbL-V9305_pgt002_p2 psbL-V9305_pgt002 TTCACGCATTAGCAGTTCCT AAGTTGCTTGATCACCACGA 2073–2422 1.000 86.2
psbL-V9305_pgt002_p3 psbL-V9305_pgt002 TTCACGCATTAGCAGTTCCT CAAGTTGCTTGATCACCACG 2074–2423 1.000 85.7
psbL-V9305_pgt002_p4 psbL-V9305_pgt002 TTCACGCATTAGCAGTTCCT ACCAAGTTGCTTGATCACCA 2076–2425 1.000 85.3
psbL-V9305_pgt002_p5 psbL-V9305_pgt002 AGCCAACAGTCAAGTCAACT GGACTTGAACCCTCACGATC 1189–1240 0.400 53.3
psbJ-psaA_p1 psbJ-psaA ACCAAGAGCTGCTGTACCTA ACCACACGAACGCTTAGTTT 1756–1778 0.400 58.1
psbJ-psaA_p2 psbJ-psaA TACCAAGAGCTGCTGTACCT ACCACACGAACGCTTAGTTT 1757–1779 0.400 58.1
psbJ-psaA_p3 psbJ-psaA CCAAGAGCTGCTGTACCTAC ACCACACGAACGCTTAGTTT 1755–1777 0.400 56.2
psbJ-psaA_p4 psbJ-psaA ACCAAGAGCTGCTGTACCTA GCGTATACGGTTCTGTGGAA 1283 0.200 45.2
psbJ-psaA_p5 psbJ-psaA TACCAAGAGCTGCTGTACCT GCGTATACGGTTCTGTGGAA 1284 0.200 45.2
rpl20-rbcL_p1 rpl20-rbcL ATAATGAAGCTGCTCCACGG CCTGGTTGTGGAGTCATACG 882–1001 0.800 83.6
rpl20-rbcL_p2 rpl20-rbcL ATAATGAAGCTGCTCCACGG CTGGTTGTGGAGTCATACGG 881–1000 0.800 83.6
rpl20-rbcL_p3 rpl20-rbcL ATAATGAAGCTGCTCCACGG GCACGAAGAGCTTTGAAACC 1137–1256 0.800 83.4
rpl20-rbcL_p4 rpl20-rbcL ATAATGAAGCTGCTCCACGG TCTCTCCAACGCATGAATGG 1389–1472 0.600 73.9
rpl20-rbcL_p5 rpl20-rbcL ATAATGAAGCTGCTCCACGG GGTCTCTCCAACGCATGAAT 1391–1474 0.600 73.9

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
Tetradesmus arenicola NC_086756.1 151685 View on NCBI ↗
Tetradesmus bajacalifornicus NC_086755.1 156181 View on NCBI ↗
Tetradesmus dissociatus f. oviformis OR502667.1 168621 View on NCBI ↗
Tetradesmus distendus NC_086753.1 167631 View on NCBI ↗
Tetradesmus lancea OR502671.1 174598 View on NCBI ↗