Markers + reference

Erigeron

15 species · Asteraceae · Asterales

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Species 15
Genome length 152–153 kb
Candidate markers 266
Primer pairs 95

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-trnC-GCA LSC 778 0.0113 1.00 60.0 yes View details
trnG-UCC-psbD LSC 1767 0.0120 0.97 72.3 yes View details
trnT-UGU-trnL-UAA LSC 638 0.0172 1.00 74.4 yes View details
ndhC-trnV-UAC LSC 688 0.0153 0.99 79.1 yes View details
accD-psaI LSC 954 0.0101 0.99 71.7 yes View details
ycf4-cemA LSC 977 0.0116 0.97 71.3 yes View details
rpl16 LSC 1529 0.0072 1.00 65.8 yes View details
rps19 LSC 279 0.0116 1.00 39.0 yes View details
rpl32-ndhF SSC 1091 0.0156 1.00 72.9 yes View details
rps19 IRa 67 0.0037 1.00 30.8 no View details
rpl22-rps19 LSC 136 0.0510 0.95 70.4 yes View details
trnK-rps16 LSC 854 0.0078 1.00 68.1 yes View details
ndhD-ccsA SSC 274 0.0245 1.00 68.0 yes View details
ndhF-ycf1 SSC 22 0.1153 1.00 65.8 yes View details
trnG-UCC-trnfM-CAU LSC 244 0.0165 1.00 65.7 yes View details
trnR-UCU-trnG-UCC LSC 289 0.0193 0.87 65.1 yes View details
ycf3-trnS-GGA LSC 872 0.0063 1.00 64.3 yes View details
trnL-UAG-rpl32 SSC 613 0.0069 1.00 64.1 yes View details
clpP-psbB LSC 570 0.0126 0.96 63.0 yes View details
trnE-UUC-rpoB LSC 1058 0.0063 0.99 62.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-rps16_p1 trnK-rps16 TCCTAGCCGCACTTAAAAGC TTCCTTGAAAAAGGCGCTCA 963–1004 1.000 80.9
trnK-rps16_p2 trnK-rps16 CCGCACTTAAAAGCCGAGTA TTCCTTGAAAAAGGCGCTCA 957–998 1.000 80.8
trnK-rps16_p3 trnK-rps16 TCGCGGTCTTCCAAACTTTA TTCCTTGAAAAAGGCGCTCA 1029–1070 1.000 78.5
trnK-rps16_p4 trnK-rps16 CGCGGTCTTCCAAACTTTAC TTCCTTGAAAAAGGCGCTCA 1028–1069 1.000 78.0
trnK-rps16_p5 trnK-rps16 TCCTAGCCGCACTTAAAAGC TCCTTGAAAAAGGCGCTCAG 962–1003 1.000 77.3
trnS-trnC-GCA_p1 trnS-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 924–969 1.000 81.8
trnS-trnC-GCA_p2 trnS-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 906–951 1.000 79.7
trnS-trnC-GCA_p3 trnS-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 860–905 1.000 78.2
trnS-trnC-GCA_p4 trnS-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 925–970 1.000 77.6
trnS-trnC-GCA_p5 trnS-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 842–887 1.000 76.1
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 1154–1226 1.000 68.5
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 1113–1185 1.000 67.9
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 1144–1216 1.000 67.7
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 1149–1221 1.000 67.7
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 1144–1216 1.000 67.2
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 305–369 1.000 74.5
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 308–372 1.000 74.2
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 311–375 1.000 73.7
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 314–378 1.000 73.4
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 309–373 1.000 72.0
trnG-UCC-psbD_p1 trnG-UCC-psbD ATGAAACCGAAAGACCCCTT GAAACGGTCCCTACGTAACC 1480–1927 1.000 80.8
trnG-UCC-psbD_p2 trnG-UCC-psbD AATGAAACCGAAAGACCCCT GAAACGGTCCCTACGTAACC 1481–1928 1.000 80.7
trnG-UCC-psbD_p3 trnG-UCC-psbD GAATGAAACCGAAAGACCCCT GAAACGGTCCCTACGTAACC 1482–1929 1.000 78.9
trnG-UCC-psbD_p4 trnG-UCC-psbD AATGAAACCGAAAGACCCCT GGACCAGCCTACAAAAACGA 1499–1946 0.933 76.2
trnG-UCC-psbD_p5 trnG-UCC-psbD ATGAAACCGAAAGACCCCTT GGACCAGCCTACAAAAACGA 1498–1945 0.933 76.2
trnG-UCC-trnfM-CAU_p1 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG CTTGAGGTCACGGGTTCAAA 279–400 1.000 87.0
trnG-UCC-trnfM-CAU_p2 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG GGGTAGAGCAGTTTGGTAGC 315–436 1.000 86.6
trnG-UCC-trnfM-CAU_p3 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG GTCACGGGTTCAAATCCTGT 273–394 1.000 86.5
trnG-UCC-trnfM-CAU_p4 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG TTCAGTTCTTCTCTTCGGCG 337–458 1.000 86.0
trnG-UCC-trnfM-CAU_p5 trnG-UCC-trnfM-CAU TCTTTGCCAAGGAGAAGACG TCACGGGTTCAAATCCTGTC 272–393 1.000 85.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Erigeron acris BK070975.1 152438 View on NCBI ↗
Erigeron alpiniformis BK070964.1 152258 View on NCBI ↗
Erigeron alpinus BK070965.1 152433 View on NCBI ↗
Erigeron borealis BK070966.1 152305 View on NCBI ↗
Erigeron compositus BK070967.1 152421 View on NCBI ↗
Erigeron denalii BK070968.1 152270 View on NCBI ↗
Erigeron elatus BK070969.1 152108 View on NCBI ↗
Erigeron elongatus BK070970.1 152457 View on NCBI ↗
Erigeron humilis BK070963.1 152300 View on NCBI ↗
Erigeron hyperboreus BK070971.1 152788 View on NCBI ↗
Erigeron muirii BK070972.1 153430 View on NCBI ↗
Erigeron peregrinus BK070973.1 152631 View on NCBI ↗
Erigeron philadelphicus BK070976.1 153151 View on NCBI ↗
Erigeron silenifolius BK070974.1 152420 View on NCBI ↗
Erigeron uniflorus subsp. uniflorus BK070977.1 152309 View on NCBI ↗