Markers + reference

Alfredia

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 267
Primer pairs 85

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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0019 1.00 59.8 yes View details
trnC-GCA-petN LSC 835 0.0012 1.00 59.8 yes View details
rpoB LSC 3183 0.0009 1.00 55.9 yes View details
rpl20 LSC 381 0.0026 1.00 45.8 yes View details
ycf1 SSC 5304 0.0017 1.00 45.5 yes View details
trnL-UAG-rpl32 SSC 866 0.0046 1.00 61.4 yes View details
trnF-GAA-ndhJ LSC 693 0.0000 0.97 61.4 yes View details
atpB-rbcL LSC 773 0.0000 0.98 60.3 yes View details
ndhF-trnN-GUU IRa 906 0.0022 1.00 60.0 yes View details
matK LSC 1521 0.0020 1.00 59.8 yes View details
trnK-UUU-rps16 LSC 795 0.0013 1.00 59.5 yes View details
rps16-trnQ-UUG LSC 935 0.0011 1.00 59.4 yes View details
atpI-atpH LSC 1137 0.0009 1.00 59.3 yes View details
ndhC-trnV-UAC LSC 1148 0.0009 1.00 59.3 yes View details
psbC LSC 1422 0.0007 1.00 59.2 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
psbA_p1 psbA AACAAGAGGGAAGCTATTGC TTGAAAATTCGTGCGCTTGG 1180 1.000 60.0
psbA_p2 psbA AACAAGAGGGAAGCTATTGC ATATTGGTTGACACGGGCAT 1245 1.000 58.4
psbA_p3 psbA AACAAGAGGGAAGCTATTGC ATTGGTTGACACGGGCATAT 1243 1.000 58.4
psbA_p4 psbA AAACAAGAGGGAAGCTATTGC TTGAAAATTCGTGCGCTTGG 1181 1.000 58.2
psbA_p5 psbA AAACAAGAGGGAAGCTATTGC ATTGGTTGACACGGGCATAT 1244 1.000 56.6
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACATACCCT 2754–2755 1.000 40.1
trnK-UUU_p2 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACATACCCTT 2754–2755 1.000 40.1
trnK-UUU_p3 trnK-UUU GCCCGTGTCAACCAATATCT TTCTGATTGTATCTACATACCCT 2755–2756 1.000 40.1
trnK-UUU_p4 trnK-UUU TGCCCGTGTCAACCAATATC TCTGATTGTATCTACATACCCT 2755–2756 1.000 40.1
trnK-UUU_p5 trnK-UUU TGCCCGTGTCAACCAATATC TCTGATTGTATCTACATACCCTT 2755–2756 1.000 40.1
matK_p1 matK GTGATCAAATTTTTATTTACAACG ACCCCCAAAATCCTCTACCT 1598 1.000 40.2
matK_p2 matK GTGATCAAATTTTTATTTACAACG AACCCCCAAAATCCTCTACC 1599 1.000 40.2
matK_p3 matK GTGATCAAATTTTTATTTACAACG AACCCCCAAAATCCTCTACCT 1599 1.000 40.2
matK_p4 matK GTGATCAAATTTTTATTTACAACG ACCCCCAAAATCCTCTACCTT 1598 1.000 40.2
matK_p5 matK GTGATCAAATTTTTATTTACAACG CCCCCAAAATCCTCTACCTT 1597 1.000 40.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 992 1.000 76.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 991 1.000 76.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 931 1.000 76.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 930 1.000 76.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1016 1.000 75.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1008–1045 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGCTTTCTACCGCATCGTTT GAGGTTCGAATCCTTCCGTC 997–1034 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TTGCTTTCTACCGCATCGTT GAGGTTCGAATCCTTCCGTC 998–1035 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1023–1060 1.000 76.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1022–1059 1.000 76.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 888–891 1.000 78.5
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 906–909 1.000 76.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 887–890 1.000 72.6
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 896–899 1.000 72.5
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 945–948 1.000 71.8

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
Alfredia acantholepis BK071820.1 153156 View on NCBI ↗
Alfredia cernua BK071821.1 153151 View on NCBI ↗