Markers + reference

Echinacea

9 species · Asteraceae · Asterales

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Species 9
Genome length 152–152 kb
Candidate markers 270
Primer pairs 100

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 378 0.0076 1.00 48.5 yes View details
trnC-GCA-petN LSC 837 0.0046 0.99 51.6 yes View details
trnT-GGU-psbD LSC 1201 0.0024 1.00 43.4 yes View details
ycf3-trnS-GCU LSC 899 0.0142 1.00 65.1 yes View details
trnT-UGU-trnL-UAA LSC 587 0.0083 0.96 60.3 yes View details
ycf4-cemA LSC 850 0.0041 1.00 44.6 yes View details
petA-psbJ LSC 806 0.0050 1.00 47.8 yes View details
trnP-UGG-psaJ LSC 319 0.0101 1.00 47.7 yes View details
clpP-psbB LSC 473 0.0082 1.00 54.5 yes View details
trnL-UAG-rpl32 SSC 756 0.0077 1.00 59.6 yes View details
ndhF-ycf1 SSC 35 0.0379 0.97 62.8 yes View details
psbC-trnS-UGA LSC 246 0.0114 1.00 60.8 yes View details
rpl32-ndhF SSC 843 0.0015 0.99 57.3 yes View details
psbI-trnS-GCU LSC 136 0.0090 1.00 55.6 yes View details
trnR-UCU-trnG-UCC LSC 221 0.0069 1.00 52.5 yes View details
atpI-atpH LSC 1138 0.0013 1.00 52.3 yes View details
rpl16-rps3 LSC 1182 0.0012 1.00 52.3 yes View details
psaA-ycf3 LSC 718 0.0035 1.00 52.1 yes View details
psbT-psbN LSC 73 0.0183 1.00 51.3 yes View details
rpoC2-rps2 LSC 258 0.0013 0.97 49.7 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 100 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 CCGTGCTAACCTTGGTATGG 490–502 1.000 79.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 504–516 1.000 79.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 503–515 1.000 79.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 505–517 1.000 79.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 491–503 1.000 78.8
psbI-trnS-GCU_p1 psbI-trnS-GCU GCAATCCTGGACGTGAAGAA ATTGGGAGAGATGGCTGAGT 249–258 1.000 81.1
psbI-trnS-GCU_p2 psbI-trnS-GCU CCAATGATCCAGGACGCAAT ATTGGGAGAGATGGCTGAGT 264–273 1.000 79.9
psbI-trnS-GCU_p3 psbI-trnS-GCU GCAATCCTGGACGTGAAGAA CGAGTTATTCGTACCGAGGG 197–206 1.000 79.7
psbI-trnS-GCU_p4 psbI-trnS-GCU CCAATGATCCAGGACGCAAT CGAGTTATTCGTACCGAGGG 212–221 1.000 78.4
psbI-trnS-GCU_p5 psbI-trnS-GCU GCAATCCTGGACGTGAAGAA GATGGCTGAGTGGACGAAAG 240–249 1.000 77.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 876–893 1.000 81.0
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 894–911 1.000 78.8
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 875–892 1.000 75.1
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 884–901 1.000 75.0
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 933–950 1.000 74.2
rpoC2-rps2_p1 rpoC2-rps2 TGCCTTTCAAAGAATTTCCATGA CCATGGCCAAAATGAACTCC 363–374 1.000 47.0
rpoC2-rps2_p2 rpoC2-rps2 TGCCTTTCAAAGAATTTCCATGA GGCCAAAATGAACTCCTGCT 359–370 1.000 46.5
rpoC2-rps2_p3 rpoC2-rps2 TCTTGCCTTTCAAAGAATTTCCA CCATGGCCAAAATGAACTCC 366–377 1.000 46.4
rpoC2-rps2_p4 rpoC2-rps2 TCTTGCCTTTCAAAGAATTTCCA GGCCAAAATGAACTCCTGCT 362–373 1.000 46.0
rpoC2-rps2_p5 rpoC2-rps2 TGCCTTTCAAAGAATTTCCATGA TGGCCAAAATGAACTCCTGC 360–371 1.000 44.2
atpI-atpH_p1 atpI-atpH CCCGTCATGTTCCTTGGATT ATAACGGAAGCGGCAGAAAT 1269–1283 1.000 79.4
atpI-atpH_p2 atpI-atpH CCCGTCATGTTCCTTGGATT TACCTTGACCAACTCCAGGT 1325–1339 1.000 78.8
atpI-atpH_p3 atpI-atpH CCCGTCATGTTCCTTGGATT AGCCAATCCAGCAGCAATAA 1285–1299 1.000 78.5
atpI-atpH_p4 atpI-atpH CCCGTCATGTTCCTTGGATT AATAACGGAAGCGGCAGAAA 1270–1284 1.000 78.3
atpI-atpH_p5 atpI-atpH CCCGTCATGTTCCTTGGATT GCAGTACCTTGACCAACTCC 1329–1343 1.000 78.2
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 296–301 1.000 67.1
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 299–304 1.000 66.8
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 302–307 1.000 66.4
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 305–310 1.000 66.1
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 300–305 1.000 64.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Echinacea angustifolia NC_034324.1 151935 View on NCBI ↗
Echinacea atrorubens NC_034323.1 151912 View on NCBI ↗
Echinacea laevigata NC_034322.1 151886 View on NCBI ↗
Echinacea pallida NC_034321.1 151883 View on NCBI ↗
Echinacea paradoxa NC_034320.1 151837 View on NCBI ↗
Echinacea purpurea NC_034327.1 151913 View on NCBI ↗
Echinacea sanguinea NC_034328.1 151926 View on NCBI ↗
Echinacea speciosa NC_034325.1 151860 View on NCBI ↗
Echinacea tennesseensis NC_034326.1 151877 View on NCBI ↗