Markers + reference

Carum

2 species · Apiaceae · Apiales

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Species 2
Genome length 154–155 kb
Candidate markers 273
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 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
psbA LSC 1062 0.5076 0.86 81.2 yes View details
psbA-trnK-UUU LSC 226 0.4332 0.96 76.4 yes View details
trnK-UUU-rps16 LSC 531 0.0952 0.91 79.4 yes View details
trnE-UUC-trnT-GGU LSC 747 0.1138 0.93 83.0 yes View details
ycf3-trnS-GGA LSC 842 0.0680 0.79 73.4 yes View details
trnT-UGU-trnL-UAA LSC 732 0.0627 0.96 82.8 yes View details
rpl32-trnL-UAG SSC 912 0.0779 0.93 79.8 yes View details
petN-psbM LSC 1150 0.0498 0.96 84.8 yes View details
atpF-atpH LSC 315 0.0594 0.91 82.0 yes View details
rpl22-rps19 LSC 63 0.0484 0.98 81.8 yes View details
petA-psbJ LSC 956 0.0725 0.65 80.8 yes View details
ndhF-rpl32 SSC 1011 0.0504 0.94 80.1 yes View details
trnC-GCA-petN LSC 698 0.0519 0.80 79.5 yes View details
trnY-GUA-trnE-UUC LSC 87 0.5422 0.95 77.0 yes View details
psbE-petL LSC 1009 0.0450 0.99 76.6 yes View details
rbcL-accD LSC 648 0.0397 0.93 76.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA CCCCGCCGAGATTGAAAATA AAATTCGTGTGCTTGGGAGT 1227 0.500 59.5
psbA_p2 psbA CCTTCCTTCCAGGGTCTGTA AAATTCGTGTGCTTGGGAGT 1349 0.500 59.5
psbA_p3 psbA TCCAGGGTCTGTAATCCGTT AAATTCGTGTGCTTGGGAGT 1342 0.500 59.4
psbA_p4 psbA TTCCAGGGTCTGTAATCCGT AAATTCGTGTGCTTGGGAGT 1343 0.500 59.4
psbA_p5 psbA CCCCGCCGAGATTGAAAATA TGCTTGGGAGTCCCTGATAA 1218 0.500 59.4
psbA-trnK-UUU_p1 psbA-trnK-UUU CAGACGGAAACTAAGCTCCC AAGGCGGTTTGGACTGATTT 1274 0.500 59.9
psbA-trnK-UUU_p2 psbA-trnK-UUU CCAGACGGAAACTAAGCTCC AAGGCGGTTTGGACTGATTT 1275 0.500 59.9
psbA-trnK-UUU_p3 psbA-trnK-UUU CCCAGACGGAAACTAAGCTC AAGGCGGTTTGGACTGATTT 1276 0.500 59.9
psbA-trnK-UUU_p4 psbA-trnK-UUU CGGAAACTAAGCTCCCACTC AAGGCGGTTTGGACTGATTT 1270 0.500 59.9
psbA-trnK-UUU_p5 psbA-trnK-UUU AGCAGCAATGAAGGCGATAA AAGGCGGTTTGGACTGATTT 1028 0.500 59.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CTCAGCCCACAAGAACTGTT 716–887 1.000 88.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG CGATTCAAAGTGTATCGCGC 1411 0.500 59.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GATTCAAAGTGTATCGCGCG 1410 0.500 59.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGATTCAAAGTGTATCGCGC 1410 0.500 59.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GATTCAAAGTGTATCGCGCG 1409 0.500 59.8
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 406–431 1.000 84.3
atpF-atpH_p2 atpF-atpH CCAGTGGCCTAAAGAAACGA GCCTGGTTGTAGCATTAGCA 379–404 1.000 84.0
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 408–433 1.000 82.9
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGAGGCGGAGGGAAAAATAC 477–502 1.000 82.5
atpF-atpH_p5 atpF-atpH CCAGTGGCCTAAAGAAACGA TGAGGCGGAGGGAAAAATAC 450–475 1.000 82.2
trnC-GCA-petN_p1 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGCCCAAGCGAGACTTACTA 657–794 1.000 85.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 617–754 1.000 85.5
trnC-GCA-petN_p3 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGAGTCCACTTCTTCCCCAT 718–855 1.000 83.6
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 678–815 1.000 83.6
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 635–772 1.000 83.2
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1310–1324 1.000 74.2
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1249–1263 1.000 72.9
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACTGCTTTTCTGCT 1289–1303 1.000 71.3
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1310–1324 1.000 70.0
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCTTTTCTGCT 1228–1242 1.000 70.0

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
Carum buriaticum NC_066719.1 153697 View on NCBI ↗
Carum carvi NC_029889.1 155449 View on NCBI ↗