Markers + reference

Cichorium

2 species · Asteraceae · Asterales

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Species 2
Genome length 153–153 kb
Candidate markers 281
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnC-GCA-petN LSC 834 0.0122 0.98 67.6 yes View details
trnE-UUC-rpoB LSC 852 0.0082 1.00 53.9 yes View details
rpoC1 LSC 2806 0.0025 1.00 57.5 yes View details
atpI-atpH LSC 1140 0.0088 0.99 64.6 yes View details
trnT-TGT-trnL-UAA LSC 561 0.0090 0.99 64.0 yes View details
accD LSC 1407 0.0156 1.00 56.1 yes View details
trnS-GCU-trnC-GCA LSC 778 0.0026 0.97 62.0 yes View details
trnI-GAU-rrn16S SSC 293 NA 0.66 61.8 no View details
ndhC-trnV-UAC LSC 1165 0.0043 1.00 61.6 yes View details
psbM-trnD-GUC LSC 667 0.0030 0.99 61.5 yes View details
trnF-GAA-ndhJ LSC 625 0.0048 1.00 61.5 yes View details
trnK-UUU-rps16 LSC 793 0.0063 1.00 61.3 yes View details
psbE-petL LSC 1285 0.0024 0.98 61.3 yes View details
atpB-rbcL LSC 758 0.0040 1.00 61.2 yes View details
rps16-trnQ-UUG LSC 977 0.0041 1.00 61.1 yes View details
rps16 LSC 1128 0.0027 0.99 60.9 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_p1 trnK-UUU ATATGCCCGTGTCAACCAAT TGGGTTCGTTGGATTAGCTT 2971–2979 1.000 70.0
trnK-UUU_p2 trnK-UUU ATATGCCCGTGTCAACCAAT GATGGGTTCGTTGGATTAGCT 2973–2981 1.000 68.3
trnK-UUU_p3 trnK-UUU ATATGCCCGTGTCAACCAAT ATGGGTTCGTTGGATTAGCT 2972–2980 1.000 68.1
trnK-UUU_p4 trnK-UUU ATATGCCCGTGTCAACCAAT TCAAATGATGGGTTCGTTGGA 2979–2987 1.000 67.7
trnK-UUU_p5 trnK-UUU ATGCCCGTGTCAACCAATAC TGGGTTCGTTGGATTAGCTT 2969 0.500 48.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 996–1001 1.000 77.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 995–1000 1.000 77.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 936–941 1.000 77.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 935–940 1.000 77.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1020–1025 1.000 76.6
rps16_p1 rps16 AGAGCAAGAAAAGAAGGAAA TCTCTGTACCGACTGAACCA 1297–1310 1.000 40.6
rps16_p2 rps16 AGAGCAAGAAAAGAAGGAAAT TCTCTGTACCGACTGAACCA 1297–1310 1.000 40.6
rps16_p3 rps16 AGAGCAAGAAAAGAAGGAAA GTCTCTGTACCGACTGAACC 1298–1311 1.000 40.6
rps16_p4 rps16 AGAAATCACTATCCTACCCTTAGT TCTCTGTACCGACTGAACCA 1238–1251 1.000 40.6
rps16_p5 rps16 AGAAATCACTATCCTACCCT TCTCTGTACCGACTGAACCA 1238–1251 1.000 40.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1050 1.000 78.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1065 1.000 76.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1064 1.000 76.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1054 1.000 73.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1080 1.000 73.7
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 907–929 1.000 80.2
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 889–911 1.000 78.1
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 843–865 1.000 76.5
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 908–930 1.000 76.0
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 825–847 1.000 74.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 891–893 1.000 80.5
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 909–911 1.000 78.2
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 890–892 1.000 74.5
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 899–901 1.000 74.4
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 948–950 1.000 73.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Cichorium endivia NC_082974.1 152809 View on NCBI ↗
Cichorium intybus NC_043842.1 152975 View on NCBI ↗