Markers + reference

Pediastrum

2 species · Hydrodictyaceae · Sphaeropleales

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Species 2
Genome length 220–233 kb
Candidate markers 283
Primer pairs 135

Genome-wide nucleotide diversity

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

Candidate markers

16 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl32-rps2 LSC 1778 0.2765 0.52 72.5 yes View details
DR496_pgp011 LSC 924 0.3540 0.73 77.6 yes View details
DR496_pgp013-DR496_pgp014 LSC 597 0.4338 0.54 73.7 yes View details
DR496_pgp017-ftsH LSC 716 0.3841 0.98 80.5 yes View details
ftsH-trnT(ugu) LSC 1394 0.2822 0.70 76.6 yes View details
DR496_pgp095-rpoBb LSC 1935 0.2443 0.82 78.9 yes View details
rpoBb-rpoBa LSC 1842 0.2338 0.77 81.3 yes View details
atpI-psbJ LSC 2047 0.2574 0.69 83.7 yes View details
DR496_pgp070-DR496_pgp069 IRb 282 0.4249 0.97 75.6 yes View details
DR496_pgp069 IRb 777 0.3733 0.92 82.9 yes View details
DR496_pgp068-DR496_pgp067 IRb 405 0.4509 0.93 79.1 yes View details
psbM-trnR(acg) SSC 1085 0.2952 0.76 82.7 yes View details
rps8-rpl5 SSC 890 0.3276 0.78 83.7 yes View details
DR496_pgp024-DR496_pgp023 IRa 405 0.4509 0.93 79.1 yes View details
DR496_pgp022 IRa 777 0.3733 0.92 82.9 yes View details
DR496_pgp022-DR496_pgp021 IRa 282 0.4249 0.97 75.6 yes View details
ycf1-trnS(gcu) IRa 927 0.2332 0.93 90.5 yes View details
rrl-rrf IRb 233 0.3254 0.90 89.3 yes View details
rrf-rrl IRa 233 0.3254 0.90 89.3 yes View details
trnH(gug)-trnS(uga) LSC 786 0.3769 0.95 89.1 yes View details
trnMf(cau)-chlB LSC 537 0.2455 0.94 86.2 yes View details
rrf-trnS(gcu) IRb 749 0.2176 0.70 85.3 yes View details
trnS(gcu)-rrf IRa 749 0.2176 0.70 85.3 yes View details
trnD(guc)-rps11 LSC 658 0.2968 0.94 85.2 yes View details
tufA-trnV(uac) SSC 704 0.2740 0.95 84.5 yes View details
rpl23-rpl2 SSC 760 0.1756 0.91 83.9 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 135 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl32-rps2_p1 rpl32-rps2 TTTCGTGGAGCAGCTTCTTT GATTGTTTTCCTTCGCCTGC 2464 0.500 59.6
rpl32-rps2_p2 rpl32-rps2 TCGTGGAGCAGCTTCTTTAC GATTGTTTTCCTTCGCCTGC 2462 0.500 59.2
rpl32-rps2_p3 rpl32-rps2 CGTGGAGCAGCTTCTTTACT GATTGTTTTCCTTCGCCTGC 2461 0.500 59.2
rpl32-rps2_p4 rpl32-rps2 TTGAAGCCAAGATTGTCGCT GATTGTTTTCCTTCGCCTGC 2101 0.500 59.0
rpl32-rps2_p5 rpl32-rps2 CGTGTAAATGCAGCAACTCG GATTGTTTTCCTTCGCCTGC 2344 0.500 58.8
DR496_pgp011_p1 DR496_pgp011 TCTGCCAAAATGGAAGGCTT GAAGCACCGAACCGAAAAAG 1372 0.500 59.6
DR496_pgp011_p2 DR496_pgp011 ATTGCGCTGTCCACAAATTG GAAGCACCGAACCGAAAAAG 1796 0.500 59.2
DR496_pgp011_p3 DR496_pgp011 TCTGCCAAAATGGAAGGCTT CGATCGAAGATTGTCGCTCT 1598 0.500 59.0
DR496_pgp011_p4 DR496_pgp011 TCTGCCAAAATGGAAGGCTT GCCAAAGCGAAAAACTTCGA 1673 0.500 59.0
DR496_pgp011_p5 DR496_pgp011 TCTGCCAAAATGGAAGGCTT CCGAACCGAAAAAGCGAATC 1366 0.500 58.9
DR496_pgp013-DR496_pgp014_p1 DR496_pgp013-DR496_pgp014 TTCTTCTTTCTACGCTCCGC CTGAACTGATGAAGCGCTCT 816 0.500 59.9
DR496_pgp013-DR496_pgp014_p2 DR496_pgp013-DR496_pgp014 TTCTTCTTTCTACGCTCCGC CGGTTCTTCGATTCTTCGGT 1390 0.500 59.9
DR496_pgp013-DR496_pgp014_p3 DR496_pgp013-DR496_pgp014 TTCTTCTTTCTACGCTCCGC CGCATCGGTTCAGTACTTCA 939 0.500 59.9
DR496_pgp013-DR496_pgp014_p4 DR496_pgp013-DR496_pgp014 ACTCGAGTGCGACAATCTTC CTGAACTGATGAAGCGCTCT 1445 0.500 59.8
DR496_pgp013-DR496_pgp014_p5 DR496_pgp013-DR496_pgp014 GAACTCGAGTGCGACAATCT CTGAACTGATGAAGCGCTCT 1447 0.500 59.8
DR496_pgp017-ftsH_p1 DR496_pgp017-ftsH CAAAGAGCCGAGCCAAAAAG AGAGAACCCACGCAAACAAT 1430 0.500 59.4
DR496_pgp017-ftsH_p2 DR496_pgp017-ftsH CTTCGGCAATTTCGGAATCG AGAGAACCCACGCAAACAAT 1393 0.500 59.1
DR496_pgp017-ftsH_p3 DR496_pgp017-ftsH CTCGGTTATGCCAAAGTGGA AGAGAACCCACGCAAACAAT 1465 0.500 59.0
DR496_pgp017-ftsH_p4 DR496_pgp017-ftsH TCGGTTATGCCAAAGTGGAG AGAGAACCCACGCAAACAAT 1464 0.500 59.0
DR496_pgp017-ftsH_p5 DR496_pgp017-ftsH AGCTGCTTCCTATCCCTTCA AGAGAACCCACGCAAACAAT 1495 0.500 58.9
ftsH-trnT(ugu)_p1 ftsH-trnT(ugu) GCTTCAGTTCGGTTGCTTTC AGCCTGCTTAACTCAATCGG 1794 0.500 59.5
ftsH-trnT(ugu)_p2 ftsH-trnT(ugu) GCTTCAGTTCGGTTGCTTTC GAAGAACCAACTGCGCATTC 2366 0.500 59.4
ftsH-trnT(ugu)_p3 ftsH-trnT(ugu) GGAGCAAGAACCCGAATGAT AGCCTGCTTAACTCAATCGG 1684 0.500 59.4
ftsH-trnT(ugu)_p4 ftsH-trnT(ugu) GGAGCAAGAACCCGAATGAT GAAGAACCAACTGCGCATTC 2256 0.500 59.4
ftsH-trnT(ugu)_p5 ftsH-trnT(ugu) GCTTCAGTTCGGTTGCTTTC GAGTTTTTCTTCGGCTTCGC 1908 0.500 59.3
DR496_pgp095-rpoBb_p1 DR496_pgp095-rpoBb TTCGGCTTTTGCTCCTTCTT AAGTTTGGCTATCGGCGATT 2682 0.500 59.5
DR496_pgp095-rpoBb_p2 DR496_pgp095-rpoBb GCGTTTCTTTTGCACTTGGT AAGTTTGGCTATCGGCGATT 2743 0.500 59.1
DR496_pgp095-rpoBb_p3 DR496_pgp095-rpoBb TTCGGCTTTTGCTCCTTCTT TCGTCGGCTATTTCGGAATC 2777 0.500 58.8
DR496_pgp095-rpoBb_p4 DR496_pgp095-rpoBb TTCGGCTTTTGCTCCTTCTT CTCGTCGGCTATTTCGGAAT 2778 0.500 58.8
DR496_pgp095-rpoBb_p5 DR496_pgp095-rpoBb TTCGGCTTTTGCTCCTTCTT TCAGCTAGCCTAACCGAAGA 2663 0.500 58.7

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
Pediastrum angulosum NC_037919.1 219917 View on NCBI ↗
Pediastrum duplex NC_034654.1 232554 View on NCBI ↗