Markers + reference

Conioselinum

11 species · Apiaceae · Apiales

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Species 11
Genome length 146–149 kb
Candidate markers 264
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 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD-psaI LSC 441 0.0114 0.98 46.7 yes View details
petA-psbJ LSC 969 0.0220 0.98 67.7 yes View details
ycf2 LSC 6273 0.0050 1.00 37.5 yes View details
ndhF-rpl32 SSC 1056 0.0097 0.99 54.7 yes View details
rpl32-trnL-UAG SSC 976 0.0098 0.96 52.6 yes View details
ccsA SSC 1014 0.0039 1.00 39.7 yes View details
trnL-CAA-trnH-GUG IRa 2258 0.0364 0.99 77.3 no View details
ycf1-ndhF SSC 39 0.0742 0.67 73.1 yes View details
ccsA-ndhD SSC 223 0.0344 1.00 58.0 yes View details
rpoB-trnC-GCA LSC 1218 0.0052 1.00 55.6 yes View details
ycf3-trnS-GGA LSC 825 0.0079 1.00 54.3 yes View details
atpF-atpH LSC 298 0.0155 0.99 54.0 yes View details
rps16-trnQ-UUG LSC 1247 0.0021 0.99 53.7 yes View details
rpl20-rps12 LSC 786 0.0049 0.98 52.8 yes View details
trnE-UUC-trnT-GGU LSC 770 0.0096 0.98 51.9 yes View details
trnK-UUU-rps16 LSC 716 0.0088 0.99 51.1 yes View details
ndhA SSC 2163 0.0040 1.00 50.7 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AGGAACTGTTCGGGATCTTT 835–842 1.000 70.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTGTTCGGGATCTTT 791–798 1.000 69.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTGTTCGGGATCTTT 790–797 1.000 69.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCTCGCTTCATCCAAATGT AGGAACTGTTCGGGATCTTT 834–841 1.000 68.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC AGGAACTGTTCGGGATCTTT 806–813 1.000 68.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT AAATATAGATGGGGCGTGGC 857–1366 1.000 82.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT AAATATAGATGGGGCGTGGC 858–1367 1.000 82.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAATATAGATGGGGCGTGGC 868–1377 1.000 81.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC AAATATAGATGGGGCGTGGC 883–1392 1.000 80.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG AAATATAGATGGGGCGTGGC 882–1391 1.000 80.0
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 413–479 1.000 80.1
atpF-atpH_p2 atpF-atpH CCAGTGGCCTAAAGAAACGA GCCTGGTTGTAGCATTAGCA 386–452 1.000 79.8
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 415–481 1.000 78.7
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGAGGCGGAGGGAAAAATAC 484–550 1.000 78.3
atpF-atpH_p5 atpF-atpH CCAGTGGCCTAAAGAAACGA TGAGGCGGAGGGAAAAATAC 457–523 1.000 78.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT CCGGATTTGAACTGGGGAAA 1122–1372 1.000 83.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCACGAACCTACAAAAGCC CCGGATTTGAACTGGGGAAA 1123–1373 1.000 83.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT TTATTGATCAGGCGACACCC 1140–1390 1.000 81.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCACGAACCTACAAAAGCC TTATTGATCAGGCGACACCC 1141–1391 1.000 81.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT AAAAGGATTTGCAGTCCCCC 1104–1354 1.000 81.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 824–854 1.000 82.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GTGTAGTACCCTACCCCCAG TACCGCTGAGTTAAAAGGGC 859–889 1.000 81.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGTGTAGTACCCTACCCCCA TACCGCTGAGTTAAAAGGGC 860–890 1.000 78.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGACTTACGCCTTACCATGG 852–882 1.000 77.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GCCTTACCATGGCGTTACTC 844–874 1.000 77.5
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 906–921 1.000 73.3
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 927–942 1.000 72.8
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTCAA 877–892 1.000 72.6
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA AGTTCCAATGCTACGCCTTC 879–894 1.000 72.0
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACCCTCGGTAAACAAAAGCC 907–922 1.000 70.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Conioselinum acuminatum NC_065483.1 148005 View on NCBI ↗
Conioselinum anthriscoides PV613218.1 148564 View on NCBI ↗
Conioselinum chinense ON470829.1 148494 View on NCBI ↗
Conioselinum officinale NC_039760.1 148518 View on NCBI ↗
Conioselinum pseudoangelica PV613222.1 146985 View on NCBI ↗
Conioselinum pteridophyllum NC_049056.1 146443 View on NCBI ↗
Conioselinum shanii PV613228.1 148487 View on NCBI ↗
Conioselinum sinchianum PV613229.1 148652 View on NCBI ↗
Conioselinum smithii PV613230.1 148489 View on NCBI ↗
Conioselinum tenuisectum NC_065484.1 148356 View on NCBI ↗
Conioselinum vaginatum ON470828.1 148632 View on NCBI ↗