Markers + reference

Heracleum

9 species · Apiaceae · Apiales

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Species 9
Genome length 142–150 kb
Candidate markers 252
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 252 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnT-GGU Genome 802 0.0280 0.96 69.2 yes View details
trnT-UGU-trnL-UAA Genome 772 0.0213 0.99 66.6 yes View details
ycf2-trnL-CAA Genome 632 0.1081 1.00 84.2 yes View details
trnV-GAC-rrn16 Genome 1770 0.0219 0.94 52.0 yes View details
ndhF Genome 2238 0.0079 1.00 43.2 yes View details
ndhF-rpl32 Genome 968 0.0202 0.97 67.4 yes View details
ccsA Genome 975 0.0052 1.00 41.9 yes View details
rrn16-trnH-GUG Genome 1198 0.0626 0.92 73.5 no View details
ccsA-ndhD Genome 229 0.0486 0.97 70.9 yes View details
trnL-UAG-ccsA Genome 96 0.0370 1.00 66.0 yes View details
rps16-trnQ-UUG Genome 1255 0.0181 0.99 64.7 yes View details
psbA-trnK-UUU Genome 201 0.0374 0.99 62.4 yes View details
ycf1-ndhF Genome 31 0.1214 0.94 62.3 yes View details
rpl32-trnL-UAG Genome 920 0.0158 0.98 62.3 yes View details
petN-psbM Genome 1157 0.0134 0.99 62.1 yes View details
trnG-UCC-trnR-UCU Genome 131 0.0250 1.00 60.1 yes View details
psbB-psbT Genome 211 0.0350 1.00 59.5 yes View details
ycf3-trnS-GGA Genome 826 0.0103 1.00 59.4 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-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTAGTTCCGGGTTCGAATCC 313–322 1.000 82.8
psbA-trnK-UUU_p2 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CTAGTTCCGGGTTCGAATCC 314–323 1.000 82.3
psbA-trnK-UUU_p3 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CTAGTTCCGGGTTCGAATCC 282–291 1.000 80.8
psbA-trnK-UUU_p4 psbA-trnK-UUU TTTTCGGTGCTGGTTATCCA CTAGTTCCGGGTTCGAATCC 304–313 1.000 80.4
psbA-trnK-UUU_p5 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT ACTCCATCCGACTAGTTCCG 324–333 1.000 79.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT AAATATAGATGGGGCGTGGC 1334–1394 1.000 84.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT AAATATAGATGGGGCGTGGC 1335–1395 1.000 84.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAATATAGATGGGGCGTGGC 1345–1405 1.000 83.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC AAATATAGATGGGGCGTGGC 1360–1420 1.000 81.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG AAATATAGATGGGGCGTGGC 1359–1419 1.000 81.9
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 205–229 1.000 70.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 208–232 1.000 69.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 211–235 1.000 69.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 214–238 1.000 69.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 209–233 1.000 67.5
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT TGTAAAAACAGAAAGTCAAAATCA 1131–1223 1.000 46.5
petN-psbM_p2 petN-psbM TGGGGAAGAAGTGGACTCTA TGTAAAAACAGAAAGTCAAAATCA 1130–1222 1.000 46.5
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT GTAAAAACAGAAAGTCAAAATCA 1130–1222 1.000 46.5
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGTAAAAACAGAAAGTCAAAATC 1131–1223 1.000 46.5
petN-psbM_p5 petN-psbM TGGGGAAGAAGTGGACTCTAG TGTAAAAACAGAAAGTCAAAATCA 1130–1222 1.000 46.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GGCGAAACGAAAAGGGAAAG GAACCGATGACTTACGCCTT 1359–1395 1.000 85.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GAATGGCGAAACGAAAAGGG GAACCGATGACTTACGCCTT 1363–1399 0.889 81.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GAATGGCGAAACGAAAAGGG TGGTGATTCCAGAGACGACT 1607–1671 0.889 81.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GAATGGCGAAACGAAAAGGG GGCGTTACTCTACCGTTGAG 1338–1374 0.444 61.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CCTGTTCCCTTGTGTTGACA GAACCGATGACTTACGCCTT 1341 0.111 44.0
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 910–918 1.000 73.4
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 931–939 1.000 72.9
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTCAA 881–889 1.000 72.7
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA AGTTCCAATGCTACGCCTTC 883–891 1.000 72.1
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACCCTCGGTAAACAAAAGCC 911–919 1.000 71.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Heracleum candicans NC_045184.1 141948 View on NCBI ↗
Heracleum kingdonii PP506009.1 142595 View on NCBI ↗
Heracleum mantegazzianum OR884994.1 149380 View on NCBI ↗
Heracleum millefolium MW228410.1 150025 View on NCBI ↗
Heracleum moellendorffii NC_042242.1 149349 View on NCBI ↗
Heracleum sphondylium subsp. pyrenaicum OR896880.1 149122 View on NCBI ↗
Heracleum stenopteroides PP506006.1 142915 View on NCBI ↗
Heracleum subtomentellum NC_086708.1 141862 View on NCBI ↗
Heracleum yungningense NC_047287.1 149223 View on NCBI ↗