Markers + reference

Oedogonium

4 species · Oedogoniaceae · Oedogoniales

Back to catalogue

Species 4
Genome length 146–197 kb
Candidate markers 253
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
orf212 IRb 642 0.4818 0.00 56.9 yes View details
orf258 IRb 780 0.4664 0.05 66.8 no View details
orf258-orf532 IRb 5306 0.4598 0.12 61.6 yes View details
orf532 IRb 1602 0.4436 0.13 67.7 yes View details
orf532 IRa 1602 0.4416 0.05 66.7 no View details
orf532-orf258 IRa 5306 0.4600 0.10 61.3 yes View details
orf258 IRa 780 0.4636 0.04 66.7 yes View details
orf258-orf212 IRa 3964 0.4437 0.05 62.3 yes View details
orf212 IRa 642 0.4818 0.00 56.9 no View details
orf212-psbA IRa 1439 0.3947 0.13 68.1 yes View details
trnL(caa)-psaA SSC 588 0.1815 0.93 85.2 yes View details
orf274-atpI LSC 1385 0.0868 0.96 84.2 yes View details
ccsA LSC 993 0.1699 0.97 83.9 yes View details
orf458 LSC 1377 0.2100 0.95 83.7 yes View details
orf458-rps12 LSC 924 0.1356 0.94 83.5 yes View details
ycf1-ycf4 LSC 523 0.2132 0.98 82.7 yes View details
trnG(ucc)-trnMe(cau) LSC 146 0.1461 0.96 82.6 yes View details
psaC SSC 1873 0.1667 0.95 82.1 yes View details
psbI LSC 2515 0.1789 0.94 81.8 yes View details
rpoA SSC 1248 0.1878 0.98 81.5 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
ccsA_p1 ccsA TGACGATCATAACAAAACGA TTACATCGCCAACCGCTTTA 628 0.250 10.0
ccsA_p2 ccsA TGACGATCATAACAAAACGA GGCAAAATTCCGGGCATTTT 793 0.250 10.0
ccsA_p3 ccsA TGACGATCATAACAAAACGA TACATCGCCAACCGCTTTAT 627 0.250 10.0
ccsA_p4 ccsA ATGACGATCATAACAAAACGA TTACATCGCCAACCGCTTTA 629 0.250 10.0
ccsA_p5 ccsA TGACGATCATAACAAAACGAT TTACATCGCCAACCGCTTTA 628 0.250 10.0
orf274-atpI_p1 orf274-atpI CAGAGTGCTTATCTGGCTGG TCATTAGTAGGGGCCGCTAA 2272–2431 0.500 59.9
orf274-atpI_p2 orf274-atpI CACGTTAGGTGGAGGTTCAG TCATTAGTAGGGGCCGCTAA 2471–2630 0.500 59.7
orf274-atpI_p3 orf274-atpI CGTTAGGTGGAGGTTCAGTG TCATTAGTAGGGGCCGCTAA 2469–2628 0.500 59.7
orf274-atpI_p4 orf274-atpI CAGAGTGCTTATCTGGCTGG CCCCCAAAACGATCCATGAA 2016–2175 0.500 59.5
orf274-atpI_p5 orf274-atpI CAGAGTGCTTATCTGGCTGG AATCGCCACGGTAATAGAGC 2230–2389 0.500 59.4
trnG(ucc)-trnMe(cau)_p1 trnG(ucc)-trnMe(cau) CGACATTGGACTTGGAAGGA GGATGCTCTGACCAACTGAG 225–252 1.000 88.0
trnG(ucc)-trnMe(cau)_p2 trnG(ucc)-trnMe(cau) CGACATTGGACTTGGAAGGA ATGAAACGGATGCTCTGACC 232–259 1.000 88.0
trnG(ucc)-trnMe(cau)_p3 trnG(ucc)-trnMe(cau) CGACATTGGACTTGGAAGGA CTAGTGACATCCCGCGTATG 249–276 1.000 87.8
trnG(ucc)-trnMe(cau)_p4 trnG(ucc)-trnMe(cau) CGACATTGGACTTGGAAGGA ACCAACTGAGCTAAACAGGC 215–242 1.000 87.4
trnG(ucc)-trnMe(cau)_p5 trnG(ucc)-trnMe(cau) ACATTGGACTTGGAAGGACC GGATGCTCTGACCAACTGAG 223–250 1.000 87.1
ycf1-ycf4_p1 ycf1-ycf4 GTCATTGTTCCAATCGCAGC GGAATGTTGGAGGTGGGTTT 1310–1316 0.500 60.7
ycf1-ycf4_p2 ycf1-ycf4 GTCATTGTTCCAATCGCAGC TGTTGGAGGTGGGTTTAACG 1306–1312 0.500 60.6
ycf1-ycf4_p3 ycf1-ycf4 GCAGTCATTGTTCCAATCGC GGAATGTTGGAGGTGGGTTT 1313 0.250 49.1
ycf1-ycf4_p4 ycf1-ycf4 GCAGTCATTGTTCCAATCGC TGTTGGAGGTGGGTTTAACG 1309 0.250 49.0
ycf1-ycf4_p5 ycf1-ycf4 CGCAGTCATTGTTCCAATCG GGAATGTTGGAGGTGGGTTT 1314 0.250 48.6
psbI_p1 psbI CGATATATCGGACCCAATGGG ACCAAGCAAAGCTTCTACGA 2988 0.250 36.2
psbI_p2 psbI CGATATATCGGACCCAATGGG AACCAAGCAAAGCTTCTACGA 2989 0.250 31.3
psbI_p3 psbI CGATATATCGGACCCAATGGG ACCAAGCAAAGCTTCTACGAA 2988 0.250 31.3
psbI_p4 psbI CGATATATCGGACCCAATGGG AACCAAGCAAAGCTTCTACG 2989 0.250 29.8
psbI_p5 psbI CGATATATCGGACCCAATGGG AAACCAAGCAAAGCTTCTACG 2990 0.250 27.6
orf458_p1 orf458 GCAGATTTTCGCAAGGCATT AAAGCCAATGGTACCTAGCG 1782–1962 0.750 81.7
orf458_p2 orf458 GCAGATTTTCGCAAGGCATT GTACCCAATTTCAGGTGGCA 2148–2325 0.750 81.3
orf458_p3 orf458 GCAGATTTTCGCAAGGCATT GAGCTGGTGGATTTTCCGAA 1647–1828 0.750 80.6
orf458_p4 orf458 CCCCTAAGAACCGTACATGC AAAGCCAATGGTACCTAGCG 1929–2005 0.500 61.1
orf458_p5 orf458 CCCCTAAGAACCGTACATGC GTACCCAATTTCAGGTGGCA 2292–2368 0.500 60.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Oedogonium capilliforme MW250874.1 195349 View on NCBI ↗
Oedogonium cardiacum NC_011031.1 196547 View on NCBI ↗
Oedogonium crispum MW250872.1 146367 View on NCBI ↗
Oedogonium dentireticulatum MW250871.1 159341 View on NCBI ↗