Markers + reference

Laserpitium

2 species · Apiaceae · Apiales

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Species 2
Genome length 158–158 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 410 0.0049 1.00 51.4 yes View details
rpoB-trnC-GCA LSC 1222 0.0025 1.00 60.2 yes View details
petN-psbM LSC 1147 0.0035 0.99 61.4 yes View details
ycf3-trnS-GGA LSC 889 0.0045 1.00 61.0 yes View details
trnT-UGU-trnL-UAA LSC 823 0.0049 1.00 56.7 yes View details
accD-psaI LSC 434 0.0046 1.00 43.8 yes View details
petB LSC 1397 0.0050 1.00 61.6 yes View details
rps8 LSC 405 0.0074 1.00 58.9 yes View details
rpl16 LSC 1372 0.0022 1.00 45.5 yes View details
ndhK LSC 678 0.0029 1.00 60.4 yes View details
atpB-rbcL LSC 758 0.0026 1.00 60.4 yes View details
ndhF-rpl32 SSC 1188 0.0008 0.99 60.2 yes View details
matK LSC 1545 0.0026 1.00 60.1 yes View details
rpoA LSC 1062 0.0019 1.00 59.8 yes View details
trnT-GGU-psbD LSC 1254 0.0016 1.00 59.7 yes View details
petD LSC 1247 0.0016 1.00 59.7 yes View details
ndhH SSC 1182 0.0017 1.00 59.7 yes View details
trnC-GCA-petN LSC 652 0.0015 1.00 59.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TACATATCCCTTTTTGTGGC AGGGGTTTTTATTGAAAAGTCGA 2694 1.000 40.1
trnK-UUU_p2 trnK-UUU TACATATCCCTTTTTGTGGC ACATAAGAACTAAGAGGTGGTCT 2669 1.000 40.1
trnK-UUU_p3 trnK-UUU ATACATATCCCTTTTTGTGGC AGGGGTTTTTATTGAAAAGTCGA 2695 1.000 40.1
trnK-UUU_p4 trnK-UUU TACATATCCCTTTTTGTGGC GGGGTTTTTATTGAAAAGTCGA 2693 1.000 40.1
trnK-UUU_p5 trnK-UUU TACATATCCCTTTTTGTGGC AGGGGTTTTTATTGAAAAGTCG 2694 1.000 40.1
matK_p1 matK CAAAAAGTGGAATACTCGGTTGA ACCCCCAAAATCCTCTACCT 1684 1.000 47.7
matK_p2 matK TCAAAAAGTGGAATACTCGGTTG ACCCCCAAAATCCTCTACCT 1685 1.000 47.7
matK_p3 matK AAAGTGGAATACTCGGTTGA ACCCCCAAAATCCTCTACCT 1681 1.000 47.6
matK_p4 matK AAAAGTGGAATACTCGGTTGA ACCCCCAAAATCCTCTACCT 1682 1.000 46.4
matK_p5 matK TCAAAAAGTGGAATACTCGGT ACCCCCAAAATCCTCTACCT 1685 1.000 46.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 530–531 1.000 79.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 531–532 1.000 79.3
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 532–533 1.000 77.5
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 527–528 1.000 77.3
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 528–529 1.000 77.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CTTACCACTCGGCCATATCG 1268 1.000 78.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CCGGATTTGAACTGGGGAAA 1308 1.000 78.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGCCCTGATCCATGAACCTA CTTACCACTCGGCCATATCG 1335 1.000 78.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGCCCTGATCCATGAACCTA CCGGATTTGAACTGGGGAAA 1375 1.000 77.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCCTGATCCATGAACCTAC CTTACCACTCGGCCATATCG 1334 1.000 77.6
trnC-GCA-petN_p1 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGCCCAAGCGAGACTTACTA 748 1.000 78.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 708 1.000 78.2
trnC-GCA-petN_p3 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGAGTCCACTTCTTCCCCAT 809 1.000 76.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 769 1.000 76.6
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 726 1.000 76.1
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1313–1321 1.000 68.3
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1252–1260 1.000 66.7
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACTGCTTTTCTGCT 1292–1300 1.000 65.3
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1313–1321 1.000 64.1
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCTTTTCTGCT 1231–1239 1.000 63.7

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
Laserpitium latifolium OR896881.1 158247 View on NCBI ↗
Laserpitium peucedanoides OR884995.1 158204 View on NCBI ↗