Markers + reference

Ageratum

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–151 kb
Candidate markers 263
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnC-GCA-petN LSC 658 0.0061 1.00 61.7 yes View details
rpoC1 LSC 2783 0.0064 0.73 46.5 yes View details
ndhC-trnV-UAC LSC 970 0.0155 1.00 67.6 yes View details
accD LSC 522 0.0115 1.00 63.7 yes View details
petL-petG LSC 195 0.0000 1.00 18.8 yes View details
rps8 LSC 408 0.0000 1.00 29.3 yes View details
rps7-rps12 LSC 603 0.0000 1.00 27.7 yes View details
rps12 LSC 278 0.0252 1.00 67.0 yes View details
ndhH-ndhA SSC 1635 0.0024 1.00 44.9 yes View details
rpl32-ndhF SSC 1016 0.0059 1.00 62.2 yes View details
rps12 LSC 279 0.0000 1.00 33.8 no View details
petG LSC 105 0.0673 0.99 84.3 yes View details
ycf15 LSC 180 0.0222 1.00 65.3 yes View details
trnT-GGU-psbD LSC 1241 0.0000 0.95 63.1 yes View details
petA-psbJ LSC 801 0.0026 0.97 63.1 yes View details
rpoA LSC 930 0.0043 1.00 61.2 yes View details
trnK-UUU-rps16 LSC 761 0.0039 1.00 61.1 yes View details
trnR-UCU-trnT-GGU LSC 1155 0.0035 1.00 60.7 yes View details
ycf3-trnS-GGA LSC 889 0.0034 1.00 60.7 yes View details
atpF LSC 1277 0.0031 1.00 60.6 yes View details
ycf15 LSC 138 0.0000 0.99 53.9 no 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 GGTATGGATGAATCCCTCGC TTCCTTGAAAAAGGCGCTCA 954–955 1.000 77.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 897–898 1.000 76.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 896–897 1.000 76.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 983–984 1.000 75.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTCCTTGAAAAAGGCGCTCA 982–983 1.000 75.9
trnC-GCA-petN_p1 trnC-GCA-petN AAAAGGGGATGCAAGTACGA AGCCCAAGCGAGACTTACTA 774–787 1.000 72.2
trnC-GCA-petN_p2 trnC-GCA-petN CAAAAGGGGATGCAAGTACG AGCCCAAGCGAGACTTACTA 775–788 1.000 71.8
trnC-GCA-petN_p3 trnC-GCA-petN AGGATTCAAAAGGGGATGCA AGCCCAAGCGAGACTTACTA 781–794 1.000 71.8
trnC-GCA-petN_p4 trnC-GCA-petN AAAGGGGATGCAAGTACGAT AGCCCAAGCGAGACTTACTA 773–786 1.000 70.4
trnC-GCA-petN_p5 trnC-GCA-petN AGGATTCAAAAGGGGATGCAA AGCCCAAGCGAGACTTACTA 781–794 1.000 69.7
rpoC1_p1 rpoC1 TTCGGTTGTTCGTTCGAGAA AGAATTACAACAGCCCTGCC 2903–2907 1.000 81.4
rpoC1_p2 rpoC1 TTTCGGTTGTTCGTTCGAGA AGAATTACAACAGCCCTGCC 2904–2908 1.000 81.4
rpoC1_p3 rpoC1 TTCGGTTGTTCGTTCGAGAA ATTCCCGCTGGTAGCATAGA 2920–2924 1.000 80.4
rpoC1_p4 rpoC1 TTCGGTTGTTCGTTCGAGAA TCCCGCTGGTAGCATAGAAT 2918–2922 1.000 80.4
rpoC1_p5 rpoC1 TTTCGGTTGTTCGTTCGAGA TCCCGCTGGTAGCATAGAAT 2919–2923 1.000 80.4
atpF_p1 atpF ACAAAAAGAACTCTGTTCGA ATTTCGTCGGCTTGAATGGT 1431–1434 1.000 40.4
atpF_p2 atpF ACAAAAAGAACTCTGTTCGA GTCGGCTTGAATGGTTACCA 1426–1429 1.000 40.4
atpF_p3 atpF ACAAAAAGAACTCTGTTCGA TCGTCGGCTTGAATGGTTAC 1428–1431 1.000 40.4
atpF_p4 atpF ACAAAAAGAACTCTGTTCGA TTTCGTCGGCTTGAATGGTT 1430–1433 1.000 40.4
atpF_p5 atpF ACAAAAAGAACTCTGTTCGA TTCGTCGGCTTGAATGGTTA 1429–1432 1.000 40.4
trnR-UCU-trnT-GGU_p1 trnR-UCU-trnT-GGU AGAAGACCTCTGTCCTATCCA ACGCGTTACCATGGGATTAC 1229 1.000 63.4
trnR-UCU-trnT-GGU_p2 trnR-UCU-trnT-GGU AGGTTTAGAAGACCTCTGTCCT ACGCGTTACCATGGGATTAC 1235 1.000 62.7
trnR-UCU-trnT-GGU_p3 trnR-UCU-trnT-GGU AGAAGACCTCTGTCCTATCCA CGCGTTACCATGGGATTACT 1228 1.000 62.0
trnR-UCU-trnT-GGU_p4 trnR-UCU-trnT-GGU AGAAGACCTCTGTCCTATCCA CTTACGCGTTACCATGGGAT 1232 1.000 62.0
trnR-UCU-trnT-GGU_p5 trnR-UCU-trnT-GGU AGGTTTAGAAGACCTCTGTCCT CGCGTTACCATGGGATTACT 1234 1.000 61.3
trnT-GGU-psbD_p1 trnT-GGU-psbD GTAATCCCATGGTAACGCGT GAAACGGTCCCTACGTAACC 1319–1375 1.000 82.8
trnT-GGU-psbD_p2 trnT-GGU-psbD GTAATCCCATGGTAACGCGT GGACCAGCCTACAAAAACGA 1337–1393 1.000 81.9
trnT-GGU-psbD_p3 trnT-GGU-psbD AGTAATCCCATGGTAACGCG GAAACGGTCCCTACGTAACC 1320–1376 1.000 81.4
trnT-GGU-psbD_p4 trnT-GGU-psbD ATCCCATGGTAACGCGTAAG GAAACGGTCCCTACGTAACC 1316–1372 1.000 81.4
trnT-GGU-psbD_p5 trnT-GGU-psbD GTAATCCCATGGTAACGCGT ACAAAAACGAAACGGTCCCT 1327–1383 1.000 80.9

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
Ageratum conyzoides MK905238.1 151325 View on NCBI ↗
Ageratum houstonianum PP843013.1 151356 View on NCBI ↗