Markers + reference

Oedocladium

2 species · Oedogoniaceae · Oedogoniales

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Species 2
Genome length 155–204 kb
Candidate markers 239
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 239 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
chlB-chlL LSC 972 0.3602 0.52 73.7 yes View details
trnY(gua)-trnK(uuu) LSC 926 0.3913 0.77 78.8 yes View details
rpl23-trnS(uga) LSC 801 0.3273 0.55 75.7 yes View details
rpl14-psbD LSC 1462 0.2674 0.27 66.4 yes View details
orf229-rpoBb LSC 1405 0.1910 0.48 72.4 yes View details
rpoBb-tufA LSC 817 0.4271 0.94 83.5 yes View details
trnR(ucu)-psbA LSC 2776 0.3379 0.37 68.5 yes View details
orf252-orf482 IRb 3755 0.1703 0.27 68.9 yes View details
orf482 IRb 1449 0.3355 0.11 73.5 no View details
orf622-atpB SSC 1899 0.2513 0.62 73.7 yes View details
rpl36-trnR(ucg) SSC 979 0.4017 0.62 75.4 yes View details
petD SSC 1289 0.3981 0.42 73.1 yes View details
petB-trnG(gcc) SSC 1028 0.3535 0.51 76.7 yes View details
orf482 IRa 1449 0.3355 0.11 73.5 yes View details
orf252-ccsA IRa 1644 0.2024 0.76 93.0 no View details
rpoA SSC 1221 0.1671 0.95 86.7 yes View details
ccsA LSC 1305 0.1594 0.69 84.2 yes View details
orf476 LSC 1431 0.2307 0.97 82.6 yes View details
trnK(uuu)-trnI(cau) LSC 571 0.3381 0.74 82.5 yes View details
psaJ-trnMf(cau) LSC 97 0.1591 0.91 82.1 yes View details
psbL-psbF LSC 430 0.2336 0.96 81.7 yes View details
psbB-trnN(guu) SSC 334 0.3463 0.93 81.1 yes View details
rps12-psaJ LSC 614 0.2923 0.81 80.9 yes View details
atpH-atpF LSC 642 0.2927 0.83 80.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ccsA_p1 ccsA GGCGAATTCAGTACCCCAAT ACAATAATCGCTTCGCTCTT 1462 0.500 40.1
ccsA_p2 ccsA ATTATTTGACAGGGAGCGGC ACAATAATCGCTTCGCTCTT 1479 0.500 37.9
ccsA_p3 ccsA ACCGCGAAGAATTGCTAAGG ACAATAATCGCTTCGCTCTT 1430 0.500 35.5
ccsA_p4 ccsA CGCGAAGAATTGCTAAGGGT ACAATAATCGCTTCGCTCTT 1428 0.500 35.5
ccsA_p5 ccsA GCGAAGAATTGCTAAGGGTG ACAATAATCGCTTCGCTCTT 1427 0.500 33.8
chlB-chlL_p1 chlB-chlL GCTGCTTGGTTTTCTCGTTC CGGGCCACACATCTTCATAA 1396–1855 1.000 91.4
chlB-chlL_p2 chlB-chlL GCTGCTTGGTTTTCTCGTTC ATTACATCTTCGGGCCACAC 1406–1865 1.000 91.4
chlB-chlL_p3 chlB-chlL GCTGCTTGGTTTTCTCGTTC TTTTCACGGATAGAGGCTGC 2141 0.500 59.5
chlB-chlL_p4 chlB-chlL CAAGCTGCTTGGTTTTCTCG TTTTCACGGATAGAGGCTGC 2144 0.500 59.5
chlB-chlL_p5 chlB-chlL ATGCAGCTAAAGAATCGGCA TTTTCACGGATAGAGGCTGC 1498 0.500 59.5
trnY(gua)-trnK(uuu)_p1 trnY(gua)-trnK(uuu) ACGCCGCCTTTTAAAGAGAT TGAGTCGATTGCCTAAACCG 2214 0.500 59.1
trnY(gua)-trnK(uuu)_p2 trnY(gua)-trnK(uuu) ACGCCGCCTTTTAAAGAGAT TGTAGGAGTTGAACCCACCT 2245 0.500 58.2
trnY(gua)-trnK(uuu)_p3 trnY(gua)-trnK(uuu) ACGCCGCCTTTTAAAGAGAT TCTTGTCGGCGAATTCAGTT 1693 0.500 57.8
trnY(gua)-trnK(uuu)_p4 trnY(gua)-trnK(uuu) ACGCCGCCTTTTAAAGAGAT TTCTTGTCGGCGAATTCAGT 1694 0.500 57.8
trnY(gua)-trnK(uuu)_p5 trnY(gua)-trnK(uuu) ACGCCGCCTTTTAAAGAGAT CTCGGCCAAAAGTGCTAGAA 2194 0.500 57.6
trnK(uuu)-trnI(cau)_p1 trnK(uuu)-trnI(cau) ACCGATAAGTTCTGGGTTCG TGAGTCGATTGCCTAAACCG 532–642 1.000 86.6
trnK(uuu)-trnI(cau)_p2 trnK(uuu)-trnI(cau) ACCGATAAGTTCTGGGTTCG TGTAGGAGTTGAACCCACCT 563–673 1.000 85.8
trnK(uuu)-trnI(cau)_p3 trnK(uuu)-trnI(cau) CCGATAAGTTCTGGGTTCGA TGAGTCGATTGCCTAAACCG 531–641 1.000 84.3
trnK(uuu)-trnI(cau)_p4 trnK(uuu)-trnI(cau) TCAATGGTAGAGTACTCGGCT TGAGTCGATTGCCTAAACCG 557–667 1.000 83.8
trnK(uuu)-trnI(cau)_p5 trnK(uuu)-trnI(cau) AACCGATAAGTTCTGGGTTCG TGAGTCGATTGCCTAAACCG 533–643 1.000 83.7
rpl23-trnS(uga)_p1 rpl23-trnS(uga) GCCTAGCCTCCCGAAAATAC AATCCAGCAGCAACAACAGA 1787 0.500 58.9
rpl23-trnS(uga)_p2 rpl23-trnS(uga) GCCTAGCCTCCCGAAAATAC TTACCACTTGACTATGCCGC 1472 0.500 58.9
rpl23-trnS(uga)_p3 rpl23-trnS(uga) GCCTAGCCTCCCGAAAATAC AAGGAAAGGGAGGGATTCGA 1423 0.500 58.8
rpl23-trnS(uga)_p4 rpl23-trnS(uga) GCCTAGCCTCCCGAAAATAC AGGAAAGGGAGGGATTCGAA 1422 0.500 58.8
rpl23-trnS(uga)_p5 rpl23-trnS(uga) GCCTAGCCTCCCGAAAATAC GAAAGGGAGGGATTCGAACC 1420 0.500 58.7
atpH-atpF_p1 atpH-atpF TCTGTTGTTGCTGCTGGATT TCTGAAGCTCGTTGATCTGC 1076 0.500 59.9
atpH-atpF_p2 atpH-atpF GCGGCATAGTCAAGTGGTAA TCTGAAGCTCGTTGATCTGC 1391 0.500 59.8
atpH-atpF_p3 atpH-atpF TCGAATCCCTCCCTTTCCTT TCTGAAGCTCGTTGATCTGC 1440 0.500 59.7
atpH-atpF_p4 atpH-atpF TTCGAATCCCTCCCTTTCCT TCTGAAGCTCGTTGATCTGC 1441 0.500 59.7
atpH-atpF_p5 atpH-atpF GTTCGAATCCCTCCCTTTCC TCTGAAGCTCGTTGATCTGC 1442 0.500 59.7

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
Oedocladium carolinianum NC_031510.1 204438 View on NCBI ↗
Oedocladium prescottii MT364368.1 154978 View on NCBI ↗