Markers + reference

Desmodesmus

2 species · Scenedesmaceae · Sphaeropleales

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Species 2
Genome length 155–167 kb
Candidate markers 225
Primer pairs 65

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 225 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbD-psbA Genome 839 0.1140 0.88 87.9 yes View details
psbA Genome 3577 0.2046 0.95 79.4 yes View details
chlB-ODF51_pgt007 Genome 1852 0.0968 0.98 82.7 yes View details
atpB Genome 5345 0.0806 0.99 71.4 yes View details
rrs-psbC Genome 1168 0.0733 0.93 84.1 no View details
ODF51_pgt004-atpE Genome 177 0.0422 0.94 80.9 yes View details
ODF51_pgt015-rps4 Genome 306 0.0522 0.88 79.6 yes View details
rpoBb-rpoBa Genome 690 0.0579 0.98 78.1 yes View details
infA-psbB Genome 422 0.0357 0.86 77.3 yes View details
ODF51_pgt022-ODF51_pgt023 Genome 559 0.0429 0.96 77.2 yes View details
psbH-psbK Genome 709 0.0335 0.97 76.8 yes View details
ccsA-psaB Genome 784 0.0256 0.95 76.6 yes View details
ODF51_pgt021-psbM Genome 359 0.0398 0.98 73.6 yes View details
ODF51_pgt024 Genome 73 0.0548 1.00 73.6 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoBb-rpoBa_p1 rpoBb-rpoBa AGAGCTGACTTTCTGGGACT ACAGGTTTTGAAGCACGAGT 1402–1418 1.000 82.9
rpoBb-rpoBa_p2 rpoBb-rpoBa AGAGCTGACTTTCTGGGACT TGATTCAGGGCATGCTGTTT 1376–1392 1.000 82.6
rpoBb-rpoBa_p3 rpoBb-rpoBa TGCTCTGCAGAAAGGAAGTG CACAAACGACGCTTGACTTC 1417–1433 1.000 82.5
rpoBb-rpoBa_p4 rpoBb-rpoBa AGAGCTGACTTTCTGGGACT CACAAACGACGCTTGACTTC 1936–1952 1.000 82.4
rpoBb-rpoBa_p5 rpoBb-rpoBa CTTTCACAGAAGTGCCTCGT CACAAACGACGCTTGACTTC 1984–2000 1.000 81.5
psbD-psbA_p1 psbD-psbA CCAGTCATCAGCGTCATCAA AACGCTCACAACTTCCCATT 874–965 1.000 91.0
psbD-psbA_p2 psbD-psbA AACCAGTCATCAGCGTCATC AACGCTCACAACTTCCCATT 876–967 1.000 91.0
psbD-psbA_p3 psbD-psbA CCAGTCATCAGCGTCATCAA GCGTCTGTAGAAGCTCCTTC 847–938 1.000 90.7
psbD-psbA_p4 psbD-psbA CCAGTCATCAGCGTCATCAA GGAAGTTATGCACGAGCGTA 893–984 1.000 90.4
psbD-psbA_p5 psbD-psbA AACCAGTCATCAGCGTCATC GGAAGTTATGCACGAGCGTA 895–986 1.000 90.4
psbA_p1 psbA ATGTCAAGGCTGTTCTTTGC TGATTGGTTTGAACGCAAAA 176 0.500 26.5
psbA_p2 psbA ATGTCAAGGCTGTTCTTTGC TTGATTGGTTTGAACGCAAA 177 0.500 26.5
psbA_p3 psbA ATGTCAAGGCTGTTCTTTGC TTTGATTGGTTTGAACGCAA 178 0.500 26.5
psbA_p4 psbA ATGTCAAGGCTGTTCTTTGC TTTTGATTGGTTTGAACGCA 179 0.500 26.5
psbA_p5 psbA ATGTCAAGGCTGTTCTTTGC TGATTGGTTTGAACGCAAAAA 176 0.500 25.0
ODF51_pgt004-atpE_p1 ODF51_pgt004-atpE GTAAAGCCACGCTGGTTTTC GCACGCTTTCAAGTTGTGAA 263–274 1.000 83.5
ODF51_pgt004-atpE_p2 ODF51_pgt004-atpE GAAAGGGAGGGATTCGAACC GCACGCTTTCAAGTTGTGAA 293–304 1.000 83.0
ODF51_pgt004-atpE_p3 ODF51_pgt004-atpE GGAAAGGGAGGGATTCGAAC GCACGCTTTCAAGTTGTGAA 294–305 1.000 83.0
ODF51_pgt004-atpE_p4 ODF51_pgt004-atpE GAAAGGGAGGGATTCGAACC AAGCACGCTTTCAAGTTGTG 295–306 1.000 82.9
ODF51_pgt004-atpE_p5 ODF51_pgt004-atpE GGAAAGGGAGGGATTCGAAC AAGCACGCTTTCAAGTTGTG 296–307 1.000 82.9
chlB-ODF51_pgt007_p1 chlB-ODF51_pgt007 CTGGACCAGCATACATCCAA CAGGATTTGAACCTGCGACT 1951–2067 1.000 81.5
chlB-ODF51_pgt007_p2 chlB-ODF51_pgt007 CTGGACCAGCATACATCCAA ATTATGAGCCCCACGAGCTA 1926–2042 1.000 80.8
chlB-ODF51_pgt007_p3 chlB-ODF51_pgt007 CTGGACCAGCATACATCCAA GAACCTGCGACTTTGGGATT 1943–2059 1.000 79.3
chlB-ODF51_pgt007_p4 chlB-ODF51_pgt007 CTGGACCAGCATACATCCAA CAGGAGCAGGATTTGAACCT 1957–2073 1.000 78.9
chlB-ODF51_pgt007_p5 chlB-ODF51_pgt007 CTGGACCAGCATACATCCAA AGGATTTGAACCTGCGACTT 1950–2066 1.000 78.5
infA-psbB_p1 infA-psbB TGGTGACAAAGTGACTGTTGA AAGTGTCATTGAACCTGCCC 557–612 1.000 72.0
infA-psbB_p2 infA-psbB TGGTGACAAAGTGACTGTTGA TGCACAGAAATTAGTCGCCC 508–563 1.000 70.8
infA-psbB_p3 infA-psbB TGGTGACAAAGTGACTGTTGA GCCCCGGGTCATTAATAACT 492–547 1.000 70.1
infA-psbB_p4 infA-psbB TGGTGACAAAGTGACTGTTGA CCCAACCAGCAACTAAAGCA 540–595 1.000 69.7
infA-psbB_p5 infA-psbB TGGTGACAAAGTGACTGTTGA TGCCCAACCAGCAACTAAAG 542–597 1.000 69.7

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
Desmodesmus abundans NC_066651.1 155193 View on NCBI ↗
Desmodesmus spinosus PV295633.1 167203 View on NCBI ↗