Markers + reference

Ageratina

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–152 kb
Candidate markers 277
Primer pairs 75

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 7 remaining regions by MarkerSeek score (out of 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpB-rbcL LSC 1004 0.2342 0.74 92.7 yes View details
rps12-ycf15 IRb 1083 0.2964 0.92 82.7 yes View details
ycf15-trnV-GAC IRb 295 0.5156 0.76 72.1 yes View details
ycf1 SSC 5052 0.1519 0.92 77.4 yes View details
ycf1 SSC 468 0.0117 0.92 51.5 no View details
ycf15-rps12 IRa 1083 0.2964 0.92 82.7 yes View details
psbM-trnD-GUC LSC 634 0.1270 0.97 96.8 yes View details
ndhE-psaC SSC 184 0.1609 0.95 85.9 yes View details
trnC-GCA-petN LSC 799 0.1041 0.91 84.8 yes View details
trnY-GUA-rpoB LSC 1069 0.1469 0.93 83.3 yes View details
rpl2 LSC 1281 0.1041 0.85 83.3 yes View details
rpl2 LSC 1281 0.1041 0.85 83.3 yes View details
trnS-GCU-trnC-GCA LSC 654 0.0891 0.94 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA TCAGAGATTCTCGCGAGTCT 1200–1253 1.000 90.5
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA AAATTAGGCTCGCCCCATTT TCAGAGATTCTCGCGAGTCT 1755–1808 1.000 89.1
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AGTGAGGGGAAGCTTTTTGG 988 0.500 58.8
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AAATTAGGCTCGCCCCATTT AGTGAGGGGAAGCTTTTTGG 1543 0.500 58.7
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA TAGTAATCCAAAGGCGGCAC 827 0.500 58.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 854–873 1.000 89.2
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CTAAAGCCCACTTCTTCCCC 917–936 1.000 88.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AAGCCCACTTCTTCCCCATA 914–933 1.000 87.4
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TAAAGCCCACTTCTTCCCCA 916–935 1.000 85.5
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 853–872 1.000 83.2
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 751–768 1.000 60.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 745–762 1.000 60.1
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 748–765 1.000 59.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCAG TTCAATAGGCAAGAGCACCG 752–769 1.000 58.4
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCA TTCAATAGGCAAGAGCACCG 752–769 1.000 57.6
trnY-GUA-rpoB_p1 trnY-GUA-rpoB GGCGGGAGAAAAGATGGAAT TCTGCCAAACCCTGATCAAC 1606–1701 1.000 90.5
trnY-GUA-rpoB_p2 trnY-GUA-rpoB GGCGGGAGAAAAGATGGAAT ACACGAACCCATATCCTTGC 2029–2124 1.000 88.6
trnY-GUA-rpoB_p3 trnY-GUA-rpoB ACCCGTCCGAACTACAAAAC ACACGAACCCATATCCTTGC 2152–2247 1.000 87.8
trnY-GUA-rpoB_p4 trnY-GUA-rpoB CACCCGTCCGAACTACAAAA ACACGAACCCATATCCTTGC 2153–2248 1.000 87.8
trnY-GUA-rpoB_p5 trnY-GUA-rpoB GGATTCCCCGACCAATCAAA ACACGAACCCATATCCTTGC 2271–2366 1.000 87.4
atpB-rbcL_p1 atpB-rbcL CTGGCGGAAAAGCTACATCT CACCAGCTTTGAATCCAACAC 922–1165 1.000 83.6
atpB-rbcL_p2 atpB-rbcL CTGGCGGAAAAGCTACATCT ACCAGCTTTGAATCCAACACT 921–1164 1.000 83.4
atpB-rbcL_p3 atpB-rbcL GGCAACCCCAGAACTAGAAG CACCAGCTTTGAATCCAACAC 849–1092 1.000 82.9
atpB-rbcL_p4 atpB-rbcL GATACGCCCCAGGTTCTTTT CACCAGCTTTGAATCCAACAC 879–1122 1.000 82.9
atpB-rbcL_p5 atpB-rbcL GGCAACCCCAGAACTAGAAG ACCAGCTTTGAATCCAACACT 848–1091 1.000 82.7
rpl2_p1 rpl2 TGTAAAGACGAAGAAAGAAATTC ACTTAATAGCATGGCGATACA 1339–1534 1.000 50.3
rpl2_p2 rpl2 TTTGTAAAGACGAAGAAAGAAA ACTTAATAGCATGGCGATACA 1341–1536 1.000 50.3
rpl2_p3 rpl2 TTTTGTAAAGACGAAGAAAGAA ACTTAATAGCATGGCGATACA 1342–1537 1.000 50.3
rpl2_p4 rpl2 TTTTTGTAAAGACGAAGAAAGA ACTTAATAGCATGGCGATACA 1343–1538 1.000 50.3
rpl2_p5 rpl2 TTGTAAAGACGAAGAAAGAAATTC ACTTAATAGCATGGCGATACA 1340–1535 1.000 50.3

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
Ageratina adenophora NC_015621.1 150698 View on NCBI ↗
Ageratina fastigiata MT793847.1 152369 View on NCBI ↗