Markers + reference

Sinocarum

8 species · Apiaceae · Apiales

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Species 8
Genome length 151–164 kb
Candidate markers 272
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 655 0.0507 1.00 84.0 yes View details
trnE-UUC-trnT-GGU LSC 745 0.0496 0.96 80.9 yes View details
trnT-GGU-psbD LSC 686 0.0433 0.99 81.9 yes View details
trnT-UGU-trnL-UAA LSC 782 0.0457 0.98 86.9 yes View details
ndhC-trnV-UAC LSC 863 0.0401 0.99 81.1 yes View details
accD-psaI LSC 448 0.0984 0.97 79.3 yes View details
psaI-ycf4 LSC 382 0.0410 1.00 79.7 yes View details
petA-psbJ LSC 659 0.0498 0.98 80.3 yes View details
ycf1 SSC 3396 0.0089 0.57 43.6 no View details
ndhF-rpl32 SSC 881 0.0572 0.94 83.0 yes View details
rpl32-trnL-UAG SSC 597 0.0557 0.99 84.3 yes View details
ycf1 SSC 5484 0.0275 1.00 61.1 yes View details
trnC-GCA-petN LSC 690 0.0403 0.99 85.7 yes View details
rps4-trnT-UGU LSC 343 0.0515 0.97 83.4 yes View details
atpF-atpH LSC 391 0.0440 0.97 82.7 yes View details
ycf3-trnS-GGA LSC 730 0.0374 0.97 81.3 yes View details
psbM-trnD-GUC LSC 621 0.0422 0.99 81.1 yes View details
rps19-trnH-GUG LSC 4 0.4286 0.98 79.3 no View details
rps15-ycf1 SSC 429 0.0542 0.94 78.8 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG CGATTCAAAGTGTATCGCGC 1509–1532 0.750 77.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GATTCAAAGTGTATCGCGCG 1508–1531 0.750 77.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGATTCAAAGTGTATCGCGC 1508–1531 0.750 77.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GATTCAAAGTGTATCGCGCG 1507–1530 0.750 77.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG GATTCAAAGTGTATCGCGCG 1456–1479 0.750 77.5
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA GCCTGGTTGTAGCATTAGCA 453–490 1.000 88.6
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG GCCTGGTTGTAGCATTAGCA 454–491 1.000 88.0
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 484–521 1.000 87.7
atpF-atpH_p4 atpF-atpH TGGCCCAAAGAAACGAAAGA TGGCCTGGTTGTAGCATTAG 455–492 1.000 87.2
atpF-atpH_p5 atpF-atpH AGTGGCCCAAAGAAACGAAA GCCTGGTTGTAGCATTAGCA 455–492 1.000 87.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 720–774 1.000 89.7
trnC-GCA-petN_p2 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGCCCAAGCGAGACTTACTA 760–814 1.000 89.4
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 738–792 1.000 87.3
trnC-GCA-petN_p4 trnC-GCA-petN GATATGGCCGAGTGGTAAGG AGCCCAAGCGAGACTTACTA 759–813 1.000 86.3
trnC-GCA-petN_p5 trnC-GCA-petN CGATATGGCCGAGTGGTAAG GCCCAAGCGAGACTTACTAT 759–813 1.000 83.5
psbM-trnD-GUC_p1 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 706–791 1.000 48.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AATGCAAGAATATTTACTTCCAT TTCAATTGGTCAGAGCACCG 705–790 1.000 48.9
psbM-trnD-GUC_p3 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCAT TTCAATTGGTCAGAGCACCG 706–791 1.000 48.9
psbM-trnD-GUC_p4 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCA GTTCAATTGGTCAGAGCACC 707–792 1.000 48.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AATGCAAGAATATTTACTTCCAT GTTCAATTGGTCAGAGCACC 706–791 1.000 48.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 646–814 0.875 84.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CCGTTGCCTCCTTGAAAGAG TACCGCTGAGTTAAAAGGGC 647–815 0.875 79.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AAACCACTAGACGATGGGGG TACCGCTGAGTTAAAAGGGC 618–786 0.875 77.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA ACCGCTGAGTTAAAAGGGC 645–813 0.875 77.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CCGTTGCCTCCTTGAAAGA TACCGCTGAGTTAAAAGGGC 647–815 0.875 75.6
trnT-GGU-psbD_p1 trnT-GGU-psbD AAGGGCCCTTTTAACTCAGC CCAGCCTCCTAAAGCGAAAT 898–1640 1.000 89.3
trnT-GGU-psbD_p2 trnT-GGU-psbD AAGGGCCCTTTTAACTCAGC AAACTAGGCGCAAAGAACCA 1272–2014 1.000 87.7
trnT-GGU-psbD_p3 trnT-GGU-psbD AAGGGCCCTTTTAACTCAGC AACTAGGCGCAAAGAACCAA 1271–2013 1.000 87.7
trnT-GGU-psbD_p4 trnT-GGU-psbD AAGGGCCCTTTTAACTCAGC ACCAAAACTAGGCGCAAAGA 1276–2018 1.000 87.7
trnT-GGU-psbD_p5 trnT-GGU-psbD AAGGGCCCTTTTAACTCAGC CACCAAAACTAGGCGCAAAG 1277–2019 1.000 87.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Sinocarum coloratum NC_064348.1 152098 View on NCBI ↗
Sinocarum cruciatum NC_064349.1 151866 View on NCBI ↗
Sinocarum cruciatum var. linearilobum MW125617.1 151901 View on NCBI ↗
Sinocarum filicinum NC_064350.1 156925 View on NCBI ↗
Sinocarum muliense NC_083196.1 150991 View on NCBI ↗
Sinocarum schizopetalum NC_064347.1 164461 View on NCBI ↗
Sinocarum schizopetalum var. bijiangense OQ835381.1 158641 View on NCBI ↗
Sinocarum vaginatum NC_064351.1 152274 View on NCBI ↗