Markers + reference

Anthriscus

3 species · Apiaceae · Apiales

Back to catalogue

Species 3
Genome length 155–155 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1432 0.0337 0.97 73.9 yes View details
rpoB-trnC-GCA LSC 1238 0.0297 0.98 65.0 yes View details
psbM-trnD-GUC LSC 687 0.0361 1.00 74.6 yes View details
trnE-UUC-trnT-GGU LSC 713 0.0361 0.91 69.4 yes View details
ndhC-trnV-UAC LSC 1081 0.0322 0.96 71.1 yes View details
ycf4-cemA LSC 683 0.0381 0.99 69.8 yes View details
psbE-petL LSC 1132 0.0308 0.99 66.2 yes View details
rpl16 LSC 1315 0.0240 0.99 60.8 yes View details
ycf1 IRb 1667 0.0036 1.00 46.3 no View details
ndhF-rpl32 SSC 947 0.0357 0.99 72.0 yes View details
rpl32-trnL-UAG SSC 848 0.0349 0.98 74.9 yes View details
ycf1 SSC 5382 0.0216 1.00 52.2 yes View details
trnH-GUG-psbA LSC 180 0.0599 0.99 76.8 yes View details
rpl16-rps3 LSC 148 0.0616 0.99 76.4 yes View details
trnG-GCC-trnR-UCU LSC 150 0.0887 0.73 75.4 yes View details
trnS-GCU-trnG-GCC LSC 539 0.0352 0.98 75.1 yes View details
atpH-atpI LSC 1141 0.0257 1.00 75.1 yes View details
trnL-UAG-ccsA SSC 102 0.0588 1.00 74.9 yes View details
rps11-rpl36 LSC 115 0.0406 1.00 74.8 yes View details
psaJ-rpl33 LSC 446 0.0297 0.96 72.8 yes View details
trnT-UGU-trnL-UAA LSC 778 0.0318 0.97 71.8 yes View details
ndhE-ndhG SSC 230 0.0432 0.94 71.2 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 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 CCTCTAGACCTAGCTGCTGT 247–251 1.000 84.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 261–265 1.000 84.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 260–264 1.000 84.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 262–266 1.000 84.4
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC CCTCTAGACCTAGCTGCTGT 276–280 1.000 81.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT AAATATAGATGGGGCGTGGC 1551–1572 1.000 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT AAATATAGATGGGGCGTGGC 1552–1573 1.000 83.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAATATAGATGGGGCGTGGC 1562–1583 1.000 83.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC AAATATAGATGGGGCGTGGC 1577–1598 1.000 81.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG AAATATAGATGGGGCGTGGC 1576–1597 1.000 81.1
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA TGAAGGGGATTACTCGAACG 625–630 1.000 76.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA TGAAGGGGATTACTCGAACG 674–679 1.000 75.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA TTGAAGGGGATTACTCGAACG 626–631 1.000 74.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAAGGGGATTACTCGAACGA 624–629 1.000 74.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GCTTTAGTCCACTCAGCCAT TGAAGGGGATTACTCGAACG 611–616 1.000 73.9
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 183–223 1.000 73.0
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 186–226 1.000 72.7
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 189–229 1.000 72.2
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 192–232 1.000 71.9
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 187–227 1.000 70.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1203–1213 1.000 82.1
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1259–1269 1.000 81.4
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1219–1229 1.000 81.2
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 1204–1214 1.000 80.9
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 1263–1273 1.000 80.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CTTACCACTCGGCCATATCG 1941–1964 1.000 83.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CCGGATTTGAACTGGGGAAA 1981–2004 1.000 82.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG ACCTAATGCACAACCCGTTT 2107 0.333 53.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATCTTCCTCCCCAATCCGA ACCTAATGCACAACCCGTTT 1876 0.333 52.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATCTTCCTCCCCAATCCGAT ACCTAATGCACAACCCGTTT 1875 0.333 52.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Anthriscus cerefolium NC_015113.1 154719 View on NCBI ↗
Anthriscus sylvestris MT561042.1 155037 View on NCBI ↗
Anthriscus sylvestris subsp. sylvestris OR884987.1 155162 View on NCBI ↗