Markers + reference

Ahnfeltia

2 species · Ahnfeltiaceae · Ahnfeltiales

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Species 2
Genome length 190–193 kb
Candidate markers 471
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 471 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
thiG SSC 849 0.4993 0.82 79.8 yes View details
ccdA-trnN(gtt) SSC 2000 0.4708 0.81 78.8 yes View details
rne SSC 1449 0.4827 0.82 79.9 yes View details
ycf53 SSC 732 0.4894 0.90 82.3 yes View details
accD SSC 876 0.4987 0.88 81.7 yes View details
psaF SSC 576 0.4990 0.88 81.0 yes View details
ycf46 SSC 1485 0.4954 0.88 81.7 yes View details
fabH SSC 1014 0.4472 0.94 83.4 yes View details
ccs1 SSC 1308 0.4627 0.93 83.2 yes View details
ycf35-psbA SSC 606 0.4374 0.94 83.2 yes View details
ccdA SSC 726 0.4757 0.91 82.4 yes View details
ycf55 SSC 966 0.4649 0.90 82.3 yes View details
carA SSC 1152 0.4349 0.90 82.2 yes View details
cpeB-cpeA LSC 97 0.0515 1.00 81.4 yes View details
rbcR SSC 951 0.4563 0.87 81.2 yes View details
apcD SSC 486 0.4571 0.94 80.9 yes View details
ycf56 SSC 693 0.4677 0.85 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
cpeB-cpeA_p1 cpeB-cpeA GCTTCTCAACGCAAAATGGA AAGGTCAGAACTGGAAGGGA 268 1.000 74.9
cpeB-cpeA_p2 cpeB-cpeA GCTTCTCAACGCAAAATGGA AGGTCAGAACTGGAAGGGAA 267 1.000 74.9
cpeB-cpeA_p3 cpeB-cpeA AGCTTCTCAACGCAAAATGG AAGGTCAGAACTGGAAGGGA 269 1.000 74.8
cpeB-cpeA_p4 cpeB-cpeA AGCTTCTCAACGCAAAATGG AGGTCAGAACTGGAAGGGAA 268 1.000 74.8
cpeB-cpeA_p5 cpeB-cpeA GCTTCTCAACGCAAAATGGA AGCACGTTGGATATTGCCTT 298 1.000 74.7
thiG_p1 thiG TCGAAACGTAGCACCCAAAA CTTCCGGGTCCAGGAGATAT 1692 0.500 59.5
thiG_p2 thiG TCGAAACGTAGCACCCAAAA CTGGCTGGCCTAACGAATAG 2176 0.500 58.6
thiG_p3 thiG TCGAAACGTAGCACCCAAAA GGCTGGCCTAACGAATAGAG 2174 0.500 58.4
thiG_p4 thiG TCGAAACGTAGCACCCAAAA ATTGAACTGGCTGGCCTAAC 2182 0.500 58.3
thiG_p5 thiG TCGAAACGTAGCACCCAAAA ACCTGAATCAGTTGGGCTTC 1708 0.500 58.0
ccs1_p1 ccs1 ATATCTCCTGGACCCGGAAG CATACGGATCGATGGACTGC 2198 0.500 57.5
ccs1_p2 ccs1 ACTCAATACTGCAGTAGCGC CATACGGATCGATGGACTGC 2537 0.500 57.0
ccs1_p3 ccs1 CTCAATACTGCAGTAGCGCA CATACGGATCGATGGACTGC 2536 0.500 57.0
ccs1_p4 ccs1 ATATCTCCTGGACCCGGAAG CGGATCGATGGACTGCAAAT 2194 0.500 56.6
ccs1_p5 ccs1 ACTCAATACTGCAGTAGCGC CGGATCGATGGACTGCAAAT 2533 0.500 56.1
ccdA_p1 ccdA TGAAACAACTCACCACTGGG GCTTGCGAAAAATGGTGGAA 2181 0.500 58.4
ccdA_p2 ccdA ATTTCCAGAATTGTCCGCGA GCTTGCGAAAAATGGTGGAA 1763 0.500 58.0
ccdA_p3 ccdA TGAAACAACTCACCACTGGG GAGCTTGCGAAAAATGGTGG 2183 0.500 57.2
ccdA_p4 ccdA ATTTCCAGAATTGTCCGCGA GAGCTTGCGAAAAATGGTGG 1765 0.500 56.8
ccdA_p5 ccdA TGAAACAACTCACCACTGGG ATATTTCTTCGGGTGCAGCA 2147 0.500 56.2
ccdA-trnN(gtt)_p1 ccdA-trnN(gtt) GCTTTAGCTCCGGCATTAGT ACGAATATGAGCTGCTTGCA 2548 0.500 59.4
ccdA-trnN(gtt)_p2 ccdA-trnN(gtt) GCTTTAGCTCCGGCATTAGT TCAAATCCTTCCTGGGGAGT 2054 0.500 59.2
ccdA-trnN(gtt)_p3 ccdA-trnN(gtt) GCTTTAGCTCCGGCATTAGT AGCGTGTCTACCAATTCCAC 2287 0.500 58.9
ccdA-trnN(gtt)_p4 ccdA-trnN(gtt) GCTTTAGCTCCGGCATTAGT GGTTCAAATCCTTCCTGGGG 2057 0.500 58.5
ccdA-trnN(gtt)_p5 ccdA-trnN(gtt) GCTTTAGCTCCGGCATTAGT GTAGATTGAATGCGGACGGA 2351 0.500 57.9
ycf35-psbA_p1 ycf35-psbA TGCAAGCAGCTCATATTCGT AACCAATGTACAGGCGGTTT 910 0.500 59.7
ycf35-psbA_p2 ycf35-psbA TGCAAGCAGCTCATATTCGT ACCAATGTACAGGCGGTTTT 909 0.500 59.7
ycf35-psbA_p3 ycf35-psbA TGCAAGCAGCTCATATTCGT TGTGCCGGAGATACCTAGAG 1353 0.500 59.6
ycf35-psbA_p4 ycf35-psbA TGCAAGCAGCTCATATTCGT TTAGTTCATAGGGGCCACCA 1159 0.500 59.6
ycf35-psbA_p5 ycf35-psbA TGCAAGCAGCTCATATTCGT AATATCAACTGGAGGCGCAG 996 0.500 59.4

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
Ahnfeltia fastigiata NC_058737.1 193253 View on NCBI ↗
Ahnfeltia plicata NC_031145.1 190451 View on NCBI ↗