Markers + reference

Oenanthe

7 species · Apiaceae · Apiales

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Species 7
Genome length 154–155 kb
Candidate markers 273
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 794 0.0159 0.97 64.2 yes View details
atpF-atpH LSC 374 0.0280 1.00 71.7 yes View details
trnE-UUC-trnT-GGU LSC 869 0.0136 0.99 65.8 yes View details
trnT-UGU-trnL-UAA LSC 806 0.0136 0.99 66.5 yes View details
ycf4-cemA LSC 890 0.0137 1.00 61.6 yes View details
petB LSC 1406 0.0089 1.00 45.9 yes View details
ycf1 IRb 2070 0.0023 1.00 40.2 no View details
ndhF-rpl32 SSC 1175 0.0142 1.00 61.7 yes View details
ndhD SSC 1503 0.0062 1.00 43.6 yes View details
ycf1 SSC 5457 0.0082 1.00 46.1 yes View details
trnH-GUG-psbA LSC 180 0.0405 1.00 70.7 yes View details
trnC-GCA-petN LSC 708 0.0112 0.98 66.8 yes View details
trnS-UGA-psbZ LSC 376 0.0092 0.96 63.4 yes View details
rpl32-trnL-UAG SSC 544 0.0128 0.99 62.9 yes View details
trnF-GAA-ndhJ LSC 386 0.0097 1.00 61.7 yes View details
trnT-GGU-psbD LSC 1235 0.0118 1.00 60.3 yes View details
psbE-petL LSC 1216 0.0070 0.99 58.8 yes View details
clpP-psbB LSC 452 0.0084 1.00 58.7 yes View details
accD-psaI LSC 502 0.0127 0.95 58.6 yes View details
ccsA-ndhD SSC 213 0.0324 1.00 58.4 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 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 ACCGCGCTAATCTTGGTATG 301–302 1.000 83.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGCGCTAATCTTGGTATGGA 299–300 1.000 83.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ACCGCGCTAATCTTGGTATG 315–316 1.000 83.4
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC ACCGCGCTAATCTTGGTATG 314–315 1.000 83.4
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC ACCGCGCTAATCTTGGTATG 316–317 1.000 83.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AAAGGCGGAGGTTTTTAAGT 852–903 1.000 66.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAGGCGGAGGTTTTTAAGT 808–859 1.000 65.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAGGCGGAGGTTTTTAAGT 807–858 1.000 65.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AAAAGGCGGAGGTTTTTAAGT 853–904 1.000 64.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCCTCGCTTCATCCAAATGT AAAGGCGGAGGTTTTTAAGT 851–902 1.000 64.6
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA CGGAGGGAAAAATACGAGGG 525–530 1.000 85.2
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG CGGAGGGAAAAATACGAGGG 526–531 1.000 84.6
atpF-atpH_p3 atpF-atpH TGGCCCAAAGAAACGAAAGA GCCTGGTTGTAGCATTAGCA 459–464 1.000 84.5
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG CGGAGGGAAAAATACGAGGG 556–561 1.000 84.4
atpF-atpH_p5 atpF-atpH AGTGGCCCAAAGAAACGAAA CGGAGGGAAAAATACGAGGG 527–532 1.000 83.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 739–782 1.000 85.6
trnC-GCA-petN_p2 trnC-GCA-petN CGATATGGCCGAGTGGTAAG TTAAAGCAGCCCAAGCAAGA 779–822 1.000 85.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 733–776 1.000 84.2
trnC-GCA-petN_p4 trnC-GCA-petN CGATATGGCCGAGTGGTAAG CAGCCCAAGCAAGACTTACT 773–816 1.000 84.0
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 757–800 1.000 83.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 909–972 1.000 85.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 906–969 1.000 84.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA AGCTAAAGCCCCTTATCGGA 932–995 1.000 83.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TTGAACCGATGACTTACGCC 911–974 1.000 83.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTGTAGTACCCTACCCCCAG GAACCGATGACTTACGCCTT 944–1007 1.000 82.0
trnT-GGU-psbD_p1 trnT-GGU-psbD AAGGGCCCTTTTAACTCAGC TGGTAAATTTCCCAAGGGCT 1348–1392 1.000 74.8
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA TGGTAAATTTCCCAAGGGCT 1344–1388 1.000 74.6
trnT-GGU-psbD_p3 trnT-GGU-psbD TCCGATAAGGGGCTTTAGCT TGGTAAATTTCCCAAGGGCT 1286–1330 1.000 74.0
trnT-GGU-psbD_p4 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TGGTAAATTTCCCAAGGGCT 1307–1351 1.000 73.3
trnT-GGU-psbD_p5 trnT-GGU-psbD AAGGGCCCTTTTAACTCAGC TTGGTAAATTTCCCAAGGGCT 1349–1393 1.000 72.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Oenanthe hookeri PQ283867.1 154597 View on NCBI ↗
Oenanthe javanica NC_049874.1 154246 View on NCBI ↗
Oenanthe linearis PQ283871.1 154486 View on NCBI ↗
Oenanthe linearis subsp. rivularis PQ283872.1 154628 View on NCBI ↗
Oenanthe pimpinelloides PQ283874.1 154438 View on NCBI ↗
Oenanthe thomsonii PQ283875.1 154640 View on NCBI ↗
Oenanthe virgata KX832335.1 154464 View on NCBI ↗