Markers + reference

Carthamus

4 species · Asteraceae · Asterales

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Species 4
Genome length 153–153 kb
Candidate markers 267
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-rpoB LSC 951 0.0074 0.99 50.9 yes View details
trnT-GGU-psbD LSC 1186 0.0061 0.99 46.8 yes View details
psbC-trnS-UGA LSC 238 0.0151 0.97 54.5 yes View details
trnT-UGU-trnL-UAA LSC 539 0.0102 1.00 42.6 yes View details
trnL-UAA-trnF-GAA LSC 368 0.0077 0.98 39.2 yes View details
ndhC-trnV-UAC LSC 1155 0.0074 1.00 54.8 yes View details
rpl16 LSC 1432 0.0050 0.99 39.2 yes View details
ycf1 SSC 5205 0.0052 1.00 31.9 yes View details
ycf1-rps15 SSC 414 0.0109 1.00 39.8 yes View details
trnL-UAG-rpl32 SSC 843 0.0075 1.00 54.5 yes View details
rpl32-ndhF SSC 1046 0.0072 0.99 48.5 yes View details
trnG-UCC-trnT-GGU LSC 113 0.0354 1.00 63.2 yes View details
petA-psbJ LSC 813 0.0049 1.00 52.6 yes View details
accD-psaI LSC 656 0.0048 1.00 52.1 yes View details
trnR-UCU-trnG-UCC LSC 242 0.0124 1.00 51.8 yes View details
petB LSC 1420 0.0034 1.00 51.8 yes View details
clpP-psbB LSC 444 0.0071 1.00 51.2 yes View details
rrn23-rrn4.5 IRb 99 0.0118 1.00 51.0 yes View details
rrn4.5-rrn23 IRa 99 0.0118 1.00 51.0 yes View details
trnS-GCU-trnC-GCA LSC 774 0.0059 0.97 50.3 yes View details
petD LSC 1182 0.0044 1.00 50.3 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
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA GTTTGTTTATGAGGCGGCAC 942–945 1.000 81.3
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA TCAGAGATTCTCGCGAGTCT 973–976 1.000 81.2
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 922–925 1.000 80.9
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CACTCAGAGATTCTCGCGAG 976–979 1.000 80.6
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA ACTCAGAGATTCTCGCGAGT 975–978 1.000 79.4
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GAGAGAAGTCGTAACCGCTG AGTTCTTCTGTCAAACCCTGA 1036–1063 1.000 65.0
trnE-UUC-rpoB_p2 trnE-UUC-rpoB AACCCTCGTTATCTCCGTGA AGTTCTTCTGTCAAACCCTGA 1058–1085 1.000 64.5
trnE-UUC-rpoB_p3 trnE-UUC-rpoB ACCCTCGTTATCTCCGTGAA AGTTCTTCTGTCAAACCCTGA 1057–1084 1.000 64.5
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TGAACCCTCGTTATCTCCGT AGTTCTTCTGTCAAACCCTGA 1060–1087 1.000 64.5
trnE-UUC-rpoB_p5 trnE-UUC-rpoB AGAGAGAAGTCGTAACCGCT AGTTCTTCTGTCAAACCCTGA 1037–1064 1.000 64.4
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 322–329 1.000 64.8
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 325–332 1.000 64.6
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 328–335 1.000 64.1
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 331–338 1.000 63.9
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 326–333 1.000 62.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU TGAAAACCGAAAGACCCCTT ATTTGAACCGAGGGCTTACG 248 0.250 41.9
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU TGAAAACCGAAAGACCCCTT GGATTTGAACCGAGGGCTTA 250 0.250 40.8
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ATGAAAACCGAAAGACCCCT ATTTGAACCGAGGGCTTACG 249 0.250 40.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ATGAAAACCGAAAGACCCCT GGATTTGAACCGAGGGCTTA 251 0.250 38.9
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ATGAAAACCGAAAGACCCCTT ATTTGAACCGAGGGCTTACG 249 0.250 38.0
trnT-GGU-psbD_p1 trnT-GGU-psbD CGTAAGCCCTCGGTTCAAAT GGACCAGCCTACAAAAACGA 1315–1321 1.000 78.2
trnT-GGU-psbD_p2 trnT-GGU-psbD CGTAAGCCCTCGGTTCAAAT ACAAAAACGAAACGGTCCCT 1305–1311 1.000 77.2
trnT-GGU-psbD_p3 trnT-GGU-psbD TAAGCCCTCGGTTCAAATCC GGACCAGCCTACAAAAACGA 1313–1319 1.000 77.1
trnT-GGU-psbD_p4 trnT-GGU-psbD TCACTCAACCAAGCCCTTTT GGACCAGCCTACAAAAACGA 1366–1372 1.000 76.7
trnT-GGU-psbD_p5 trnT-GGU-psbD TTCACTCAACCAAGCCCTTT GGACCAGCCTACAAAAACGA 1367–1373 1.000 76.7
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 345–358 1.000 81.3
psbC-trnS-UGA_p2 psbC-trnS-UGA TCTTCGTAGGGCATTTGTGG GAGAGATGGCTGAGTGGTTG 428–441 1.000 81.2
psbC-trnS-UGA_p3 psbC-trnS-UGA TCTTCGTAGGGCATTTGTGG GTCTTTCGGAGAGATGGCTG 436–449 1.000 80.8
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GTCTTTCGGAGAGATGGCTG 353–366 1.000 80.8
psbC-trnS-UGA_p5 psbC-trnS-UGA TCTTCGTAGGGCATTTGTGG TCTTTCGGAGAGATGGCTGA 435–448 1.000 80.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Carthamus dianius BK071833.1 152769 View on NCBI ↗
Carthamus lanatus NC_085736.1 152602 View on NCBI ↗
Carthamus persicus NC_085735.1 153177 View on NCBI ↗
Carthamus tinctorius x Carthamus persicus NC_084337.1 153177 View on NCBI ↗