Markers + reference

Pedinomonas

2 species · Pedinomonadaceae · Pedinomonadales

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Species 2
Genome length 98–127 kb
Candidate markers 246
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 246 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
orf205 LSC 618 0.4730 0.75 77.9 yes View details
rbcL LSC 1428 0.4899 0.83 80.3 yes View details
atpB LSC 1443 0.4950 0.77 78.6 yes View details
psbA IRb 1059 0.4649 0.98 80.7 yes View details
psbA IRa 1059 0.4904 0.98 80.5 yes View details
psbA-atpA IRa 874 0.4806 0.80 79.4 no View details
cysA LSC 1083 0.2517 0.94 83.4 yes View details
chlI LSC 1107 0.1635 0.96 83.1 yes View details
atpA LSC 1521 0.1345 0.88 82.6 yes View details
orf105-psbA IRb 823 0.4155 0.97 81.6 yes View details
accD LSC 1146 0.1782 0.97 81.3 yes View details
orf216 LSC 651 0.4791 0.85 80.9 yes View details
psaJ-trnP(ugg) LSC 471 0.4209 0.95 80.7 yes View details
rpoA LSC 1098 0.3364 0.98 80.5 yes View details
psbC-orf105 LSC 627 0.4019 0.98 80.4 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
atpA_p1 atpA ACCTGACCAACTAAGTTGCT GCTAACCCATTCGCAGGTTA 2337 0.500 49.1
atpA_p2 atpA ACCTGACCAACTAAGTTGCT AGCCAACAAGTAATTCGCCA 1901 0.500 48.6
atpA_p3 atpA ACCTGACCAACTAAGTTGCT GTCATGGTCACGGATTTGGT 2176 0.500 48.0
atpA_p4 atpA ACCTGACCAACTAAGTTGCT CAATTGGTCATGGTCACGGA 2182 0.500 48.0
atpA_p5 atpA ACCTGACCAACTAAGTTGCT TGGTCATGGTCACGGATTTG 2178 0.500 48.0
rpoA_p1 rpoA CCGATAAAGGTGCTTGAGCT AAAGTACCCCATTTGCAGCA 1994 0.500 59.7
rpoA_p2 rpoA CCGATAAAGGTGCTTGAGCT AAGTACCCCATTTGCAGCAA 1993 0.500 59.7
rpoA_p3 rpoA CCGATAAAGGTGCTTGAGCT AGTACCCCATTTGCAGCAAA 1992 0.500 59.7
rpoA_p4 rpoA TTCTTTTTCACGCGCATCAC AAGTACCCCATTTGCAGCAA 2169 0.500 59.7
rpoA_p5 rpoA TTCTTTTTCACGCGCATCAC AGTACCCCATTTGCAGCAAA 2168 0.500 59.7
psaJ-trnP(ugg)_p1 psaJ-trnP(ugg) AGCTTCTTTCTAGCCGAACG TACCAAACTGCGCTACATCC 819 0.500 59.8
psaJ-trnP(ugg)_p2 psaJ-trnP(ugg) AGCTTCTTTCTAGCCGAACG AACCAAGTGCAAAAACTGGC 1280 0.500 59.8
psaJ-trnP(ugg)_p3 psaJ-trnP(ugg) GCTTCTTTCTAGCCGAACGA TACCAAACTGCGCTACATCC 818 0.500 59.8
psaJ-trnP(ugg)_p4 psaJ-trnP(ugg) GCTTCTTTCTAGCCGAACGA AACCAAGTGCAAAAACTGGC 1279 0.500 59.8
psaJ-trnP(ugg)_p5 psaJ-trnP(ugg) AGCTTCTTTCTAGCCGAACG AATGCAGCAGCTCGTGAATA 1466 0.500 59.8
accD_p1 accD CTGGATTCGAACCAGCGTAA TGCAACTTCCATGGCTTCTT 2119 0.500 60.0
accD_p2 accD TGGATTCGAACCAGCGTAAG TGCAACTTCCATGGCTTCTT 2118 0.500 60.0
accD_p3 accD CATCCCCATTAACCACTCGG TGCAACTTCCATGGCTTCTT 2076 0.500 59.7
accD_p4 accD CCATCCCCATTAACCACTCG TGCAACTTCCATGGCTTCTT 2077 0.500 59.7
accD_p5 accD TGGATTCGAACCAGCGTAAG ACGAACCCGAACCAATTTCA 1606 0.500 59.7
cysA_p1 cysA TGCTGGTCGTCGAGTTATTG ACTCAGTTGGTAGAGTGGCT 2399 0.500 59.8
cysA_p2 cysA AAGATGCGCCATTTAGACGT ACTCAGTTGGTAGAGTGGCT 2247 0.500 59.7
cysA_p3 cysA AGATGCGCCATTTAGACGTT ACTCAGTTGGTAGAGTGGCT 2246 0.500 59.7
cysA_p4 cysA TGCTGGTCGTCGAGTTATTG GCGGATGTTGCATAGTGGTA 1738 0.500 59.5
cysA_p5 cysA AGATGCGCCATTTAGACGTT GCGGATGTTGCATAGTGGTA 1585 0.500 59.4
orf205_p1 orf205 CAGTGAGCGGATAAGCAGAG CACAAATCACTTGCGACCAC 1546 0.500 58.5
orf205_p2 orf205 CAGTGAGCGGATAAGCAGAG TCACAAATCACTTGCGACCA 1547 0.500 58.5
orf205_p3 orf205 CGGTCAGTAGGTCAGGAGAA CACAAATCACTTGCGACCAC 1631 0.500 58.4
orf205_p4 orf205 TCTTCCGGTCAGTAGGTCAG CACAAATCACTTGCGACCAC 1636 0.500 58.4
orf205_p5 orf205 CAGTGAGCGGATAAGCAGAG GTAACTGTTCCGCGAAAAGC 1503 0.500 58.4

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
Pedinomonas minor NC_016733.1 98340 View on NCBI ↗
Pedinomonas tuberculata NC_025530.1 126694 View on NCBI ↗