Markers + reference

Atractylodes

5 species · Asteraceae · Asterales

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Species 5
Genome length 153–153 kb
Candidate markers 247
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 247 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GTG-psbA LSC 392 0.0041 1.00 50.0 yes View details
matK-rps16 LSC 1617 0.0010 1.00 45.5 yes View details
atpH-atpF LSC 374 0.0037 1.00 36.9 yes View details
trnR-TCT-trnT-GGT LSC 1149 0.0017 1.00 52.5 yes View details
trnT-TGT-trnF-GAA LSC 1437 0.0027 1.00 61.6 yes View details
ndhC-trnM-CAT LSC 2009 0.0008 1.00 51.1 yes View details
atpB-rbcL LSC 729 0.0025 1.00 62.1 yes View details
rpoA LSC 1008 0.0020 1.00 60.3 yes View details
rrn4.5S IRb 265 0.0023 1.00 35.2 yes View details
ycf1 SSC 5292 0.0012 1.00 46.2 yes View details
rpl32-ndhF SSC 1056 0.0013 1.00 59.3 yes View details
ycf1 IRa 615 0.0007 0.96 55.2 yes View details
rrn4.5S IRa 265 0.0023 1.00 35.2 no View details
trnE-TTC-rpoB LSC 900 0.0009 1.00 61.0 yes View details
trnL-TAG-rpl32 SSC 869 0.0021 1.00 52.8 yes View details
petB LSC 1677 0.0011 1.00 51.7 yes View details
ndhF SSC 2235 0.0002 0.99 50.8 yes View details
rps4-trnT-TGT LSC 378 0.0000 0.94 50.5 yes View details
clpP LSC 2014 0.0002 1.00 50.4 yes View details
rpoC1-rpoC2 LSC 120 0.0033 1.00 49.1 yes View details
rpoB LSC 3183 0.0008 1.00 48.4 yes View details
psaA-ycf3 LSC 744 0.0011 1.00 48.3 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 510–517 1.000 76.9
trnH-GTG-psbA_p2 trnH-GTG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 524–531 1.000 76.9
trnH-GTG-psbA_p3 trnH-GTG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 523–530 1.000 76.8
trnH-GTG-psbA_p4 trnH-GTG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 525–532 1.000 76.8
trnH-GTG-psbA_p5 trnH-GTG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 511–518 1.000 76.4
matK-rps16_p1 matK-rps16 TCAAGAAGGGCTCCAGAAGA CCCAGAACAAGGAAACACCA 2942–2945 1.000 79.6
matK-rps16_p2 matK-rps16 AGAAGGGCTCCAGAAGATGT CCCAGAACAAGGAAACACCA 2939–2942 1.000 79.5
matK-rps16_p3 matK-rps16 TCAAGAAGGGCTCCAGAAGA GCCGTACGAGGAGAAAACTT 2644–2647 1.000 79.5
matK-rps16_p4 matK-rps16 AGAAGGGCTCCAGAAGATGT GCCGTACGAGGAGAAAACTT 2641–2644 1.000 79.4
matK-rps16_p5 matK-rps16 TCAAGAAGGGCTCCAGAAGA AGCCGTCTATCGAATCGTTG 2573–2574 1.000 79.1
trnE-TTC-rpoB_p1 trnE-TTC-rpoB AAGTCGTAACCTCTGGACCA AGTTCTTCTGTCAAACCCTGA 997–1007 1.000 63.4
trnE-TTC-rpoB_p2 trnE-TTC-rpoB GGGAATTGAACCCTCGTTGT AGTTCTTCTGTCAAACCCTGA 1032–1042 1.000 62.6
trnE-TTC-rpoB_p3 trnE-TTC-rpoB AAGTCGTAACCTCTGGACCA TCAAACCCTGATCAATGAACCT 987–997 1.000 62.0
trnE-TTC-rpoB_p4 trnE-TTC-rpoB AAGTCGTAACCTCTGGACCA TCTTCTGTCAAACCCTGATCA 994–1004 1.000 61.7
trnE-TTC-rpoB_p5 trnE-TTC-rpoB GAACCCTCGTTGTCTCAGTG AGTTCTTCTGTCAAACCCTGA 1025–1035 1.000 61.6
rpoB_p1 rpoB CTTTGGCCTTGAATCAGGGT ACTGAGAAAGAGGGACTGCT 222 1.000 80.0
rpoB_p2 rpoB CTTTGGCCTTGAATCAGGGT GCCTTCCAATCCAGTTCCAA 257 1.000 79.4
rpoB_p3 rpoB CTTTGGCCTTGAATCAGGGT TTGGCCTTCCAATCCAGTTC 260 1.000 79.4
rpoB_p4 rpoB CTTTGGCCTTGAATCAGGGT CAATGCACTTCTCGGACTGA 237 1.000 79.4
rpoB_p5 rpoB CTTTGGCCTTGAATCAGGGT GAGAAAGAGGGACTGCTTGG 219 1.000 79.3
rpoC1-rpoC2_p1 rpoC1-rpoC2 CTATGCTACCAGCGGGAATG TAAAAGACATGAGTGGCCCG 181–199 1.000 82.0
rpoC1-rpoC2_p2 rpoC1-rpoC2 ATTCTATGCTACCAGCGGGA TAAAAGACATGAGTGGCCCG 184–202 1.000 81.3
rpoC1-rpoC2_p3 rpoC1-rpoC2 TCTATGCTACCAGCGGGAAT TAAAAGACATGAGTGGCCCG 182–200 1.000 81.3
rpoC1-rpoC2_p4 rpoC1-rpoC2 CTATGCTACCAGCGGGAATG GTTGTGCCATCAGTACCTCC 162–180 1.000 80.8
rpoC1-rpoC2_p5 rpoC1-rpoC2 TCTATGCTACCAGCGGGAAT GTTGTGCCATCAGTACCTCC 163–181 1.000 80.1
atpH-atpF_p1 atpH-atpF GCCTGGTTGTAGCATTAGCA TGGCCCAAAGAAACGAAAGA 459 1.000 78.0
atpH-atpF_p2 atpH-atpF GCCTGGTTGTAGCATTAGCA ATTAAACCCGAAACTCCCGG 490 1.000 77.5
atpH-atpF_p3 atpH-atpF GCCTGGTTGTAGCATTAGCA GTGGCCCAAAGAAACGAAAG 460 1.000 77.4
atpH-atpF_p4 atpH-atpF TGGCCTGGTTGTAGCATTAG TGGCCCAAAGAAACGAAAGA 461 1.000 76.7
atpH-atpF_p5 atpH-atpF GCCTGGTTGTAGCATTAGCA AGTGGCCCAAAGAAACGAAA 461 1.000 76.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Atractylodes chinensis NC_037484.1 153258 View on NCBI ↗
Atractylodes japonica NC_056949.1 153208 View on NCBI ↗
Atractylodes koreana NC_056987.1 153232 View on NCBI ↗
Atractylodes lancea NC_037483.1 153201 View on NCBI ↗
Atractylodes macrocephala NC_044671.1 153256 View on NCBI ↗