Markers + reference

Apium

2 species · Apiaceae · Apiales

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Species 2
Genome length 152–159 kb
Candidate markers 264
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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 3087 0.0587 0.90 78.4 yes View details
trnC-GCA-petN LSC 697 0.0604 0.38 68.2 yes View details
trnE-UUC-trnT-GGU LSC 608 0.2025 0.93 83.1 yes View details
trnT-UGU-trnL-UAA LSC 799 0.0642 0.97 79.8 yes View details
ndhC-trnV-UAC LSC 1072 0.0619 0.54 66.5 yes View details
petA-psbJ LSC 953 0.0670 0.97 78.4 yes View details
ycf1 IRb 1902 0.0079 1.00 47.5 no View details
ndhF-rpl32 SSC 942 0.0753 0.96 88.2 yes View details
rpl32-trnL-UAG SSC 570 0.0673 0.94 78.3 yes View details
ycf1 SSC 5469 0.0317 1.00 59.8 yes View details
rpl23-trnH-GUG LSC 316 0.0839 0.49 65.0 no View details
psbE-petL LSC 929 0.0495 0.93 83.8 yes View details
trnS-UGA-psbZ LSC 353 0.0540 1.00 81.2 yes View details
trnS-GCU-trnT-CGU LSC 544 0.0672 0.93 80.5 yes View details
trnT-CGU-trnR-UCU LSC 135 0.1083 0.89 80.4 yes View details
rpoB-trnC-GCA LSC 940 0.0566 0.94 79.8 yes View details
petN-psbM LSC 1097 0.0505 0.94 78.6 yes View details
trnT-GGU-psbD LSC 990 0.0555 0.98 78.6 yes View details
trnH-GUG-psbA LSC 185 0.1514 1.00 78.2 yes View details
ycf3-trnS-GGA LSC 836 0.0364 0.95 76.2 yes View details
trnD-GUC-trnY-GUA LSC 118 0.5000 0.97 75.8 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 95 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 251–278 1.000 86.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 265–292 1.000 86.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 264–291 1.000 86.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 266–293 1.000 86.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 254–281 1.000 86.4
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG TGCTTTCTACCACAGCGTTT TGGTAACATAGGTCACACCCT 915–1100 1.000 79.1
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG TTGCTTTCTACCACAGCGTT TGGTAACATAGGTCACACCCT 916–1101 1.000 79.1
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTAACATAGGTCACACCCT 926–1111 1.000 78.3
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG TCATGTCCTTCAAGTCGCAC TGGTAACATAGGTCACACCCT 937–1122 1.000 77.8
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG GGGGTTTTTCGTACCGATCA TGGTAACATAGGTCACACCCT 635 0.500 50.5
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU ATTAGCAATCCGCCGCTTTA ACCACTAAACTATACCCGCT 574–604 1.000 69.5
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU ACGGAAAGAGAGGGATTCGA ACCACTAAACTATACCCGCT 623–653 1.000 68.2
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU ATTAGCAATCCGCCGCTTTA ACTCGAACGAATCACACTTT 595–625 1.000 67.0
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU GCTTTAGTCCACTCAGCCAT ACCACTAAACTATACCCGCT 560–590 1.000 66.6
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU ATTAGCAATCCGCCGCTTTA CGAACGAATCACACTTTTACCA 592–622 1.000 66.4
trnT-CGU-trnR-UCU_p1 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 201–216 1.000 72.3
trnT-CGU-trnR-UCU_p2 trnT-CGU-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 204–219 1.000 72.0
trnT-CGU-trnR-UCU_p3 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 207–222 1.000 71.5
trnT-CGU-trnR-UCU_p4 trnT-CGU-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 210–225 1.000 71.2
trnT-CGU-trnR-UCU_p5 trnT-CGU-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 205–220 1.000 69.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTACATCTCGGAGC CTTACCACTCGGCCATATCG 985–1272 1.000 77.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCTCATTTACATCTCGGAGC CCGGATTTGAACTGGGGAAA 1025–1312 1.000 76.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTCATTTACATCTCGGAGCA CTTACCACTCGGCCATATCG 984–1271 1.000 75.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCTCATTTACATCTCGGAGCA CCGGATTTGAACTGGGGAAA 1024–1311 1.000 75.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATTTACATCTCGGAGC TTATTGATCAGGCGACACCC 1043–1330 1.000 74.7
trnC-GCA-petN_p1 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGCCCAAGCGAGACTTACTA 361–793 1.000 84.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 321–753 1.000 84.5
trnC-GCA-petN_p3 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGAGTCCACTTCTTCCCCAT 422–854 1.000 82.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 382–814 1.000 82.7
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 339–771 1.000 82.3

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
Apium graveolens NC_041087.1 152050 View on NCBI ↗
Apium leptophyllum MZ328721.1 158702 View on NCBI ↗