Markers + reference

Achillea

4 species · Asteraceae · Asterales

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Species 4
Genome length 149–151 kb
Candidate markers 273
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 380 0.0114 1.00 52.9 yes View details
rps16-trnQ-UUG LSC 908 0.0051 1.00 63.7 yes View details
trnS-GCU-trnC-GCA LSC 743 0.0056 1.00 61.6 yes View details
trnC-GCA-petN LSC 576 0.0035 1.00 39.2 yes View details
trnR-UCU-trnG-UCC LSC 175 0.0229 1.00 52.8 yes View details
trnL-UAA-trnF-GAA LSC 356 0.0029 0.98 52.2 yes View details
trnF-GAA-ndhJ LSC 704 0.0046 0.97 62.6 yes View details
petA-psbJ LSC 764 0.0092 0.99 65.8 yes View details
ycf1 IRb 591 0.0034 1.00 37.4 no View details
ndhF SSC 2232 0.0016 1.00 34.1 yes View details
ndhF-rpl32 SSC 1009 0.0036 1.00 62.1 yes View details
rpl32-trnL-UAG SSC 884 0.0068 1.00 63.2 yes View details
ycf1 SSC 5067 0.0023 1.00 41.0 yes View details
rpl14-rpl16 LSC 123 0.0122 0.98 66.4 yes View details
ndhG-ndhI SSC 359 0.0074 1.00 64.0 yes View details
petN-psbM LSC 527 0.0041 0.99 63.8 yes View details
ycf3-trnS-GGA LSC 842 0.0044 1.00 63.1 yes View details
trnK-UUU-rps16 LSC 825 0.0032 1.00 62.1 yes View details
ndhC-trnV-UAC LSC 1113 0.0018 1.00 62.1 yes View details
atpB-rbcL LSC 753 0.0033 1.00 61.6 yes View details
atpI-atpH LSC 1141 0.0018 1.00 60.1 yes View details
petB-petD LSC 863 0.0017 1.00 60.0 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 499 1.000 77.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 513 1.000 77.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 512 1.000 77.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 514 1.000 77.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 500 1.000 77.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTGAAAAAGGTGCTCAGCCT 988–1048 1.000 79.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTGAAAAAGGTGCTCAGCCT 987–1047 1.000 79.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGTGCTCAGCCT 927–987 1.000 79.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGTGCTCAGCCT 926–986 1.000 79.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AAAAGGTGCTCAGCCTACAG 983–1043 1.000 78.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 981–983 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 996–998 1.000 78.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 995–997 1.000 78.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1052–1054 1.000 76.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 985–987 1.000 75.2
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 894–917 1.000 78.8
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 876–899 1.000 76.7
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 830–853 1.000 75.0
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 895–918 1.000 74.7
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 812–835 1.000 72.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 633–634 1.000 78.6
trnC-GCA-petN_p2 trnC-GCA-petN GTATCATTTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 685–686 1.000 78.1
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 651–652 1.000 76.4
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 632–633 1.000 72.7
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 641–642 1.000 72.6
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 679–705 1.000 62.0
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 679–705 1.000 60.3
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 680–706 1.000 56.0
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 671–697 1.000 56.0
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 665–691 1.000 55.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Achillea alpina NC_067765.1 149045 View on NCBI ↗
Achillea millefolium NC_062413.1 150589 View on NCBI ↗
Achillea ptarmica PQ412534.1 149252 View on NCBI ↗
Achillea wilsoniana NC_069982.1 149133 View on NCBI ↗