Markers + reference

Euphrasia

3 species · Orobanchaceae · Lamiales

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Species 3
Genome length 118–145 kb
Candidate markers 239
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 239 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1052 0.0260 1.00 73.5 yes View details
atpF LSC 1242 0.0269 1.00 61.6 yes View details
atpF-atpH LSC 352 0.0426 1.00 68.1 yes View details
atpH-atpI LSC 955 0.0335 1.00 65.8 yes View details
rps2 LSC 711 0.0272 1.00 53.3 yes View details
rpoC2 LSC 4137 0.0196 1.00 53.4 yes View details
rpoC1 LSC 2868 0.0155 1.00 56.9 yes View details
rps2-rpoC2 LSC 226 0.0501 1.00 83.8 yes View details
trnS-GCU LSC 88 0.0530 1.00 69.5 yes View details
atpA-atpF LSC 77 0.0952 1.00 68.0 yes View details
trnC-GCA LSC 71 0.0563 1.00 64.4 yes View details
trnR-UCU LSC 72 0.0556 1.00 63.2 yes View details
trnH-GUG-psbA LSC 322 0.0405 1.00 61.4 yes View details
trnR-UCU-atpA LSC 118 0.0678 1.00 61.3 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 80 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 GAGTGGGAGCTTAGTTTCCG 1015–1016 1.000 84.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GTTATACAACGGCGGTCCTT 1088–1089 1.000 84.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGTGGGAGCTTAGTTTCCG 1029–1030 1.000 84.3
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GAGTGGGAGCTTAGTTTCCG 1028–1029 1.000 84.3
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GAGTGGGAGCTTAGTTTCCG 1030–1031 1.000 84.3
trnK-UUU_p1 trnK-UUU TCCCAATACCTATCGAAATCG TCGGATTGGATCTATACACCCT 2730 1.000 45.2
trnK-UUU_p2 trnK-UUU AGAAAATCTGGATTGCTATGCT TCGGATTGGATCTATACACCCT 2657 1.000 45.2
trnK-UUU_p3 trnK-UUU TCCCAATACCTATCGAAATCG TCGGATTGGATCTATACACCC 2730 1.000 45.2
trnK-UUU_p4 trnK-UUU TCCCAATACCTATCGAAATCG CGGATTGGATCTATACACCCT 2729 1.000 45.2
trnK-UUU_p5 trnK-UUU CCCAATACCTATCGAAATCG TCGGATTGGATCTATACACCCT 2729 1.000 45.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTGGCGTCGATTCGAAATT 1197–1207 1.000 81.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGTTGGCGTCGATTCGAAAT 1198–1208 1.000 81.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1155–1165 1.000 80.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTGTTGGCGTCGATTCGAAA 1199–1209 1.000 79.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGTTGGCGTCGATTCGAA 1200–1210 1.000 79.3
trnS-GCU_p1 trnS-GCU CCCCGGACGTGAAGAATAAA GGAACTTCCTGATTTGCGGA 286 1.000 81.4
trnS-GCU_p2 trnS-GCU AACCCCGGACGTGAAGAATA GGAACTTCCTGATTTGCGGA 288 1.000 78.7
trnS-GCU_p3 trnS-GCU ACCCCGGACGTGAAGAATAA GGAACTTCCTGATTTGCGGA 287 1.000 78.7
trnS-GCU_p4 trnS-GCU TAACCCCGGACGTGAAGAAT GGAACTTCCTGATTTGCGGA 289 1.000 78.7
trnS-GCU_p5 trnS-GCU ACCCCGGACGTGAAGAATA GGAACTTCCTGATTTGCGGA 287 1.000 76.4
trnG-UCC_p1 trnG-UCC GCTCAAGACTCTCGGTTTGA GGAATTGTATATTCAATGGTTCGCT 943 1.000 47.5
trnG-UCC_p2 trnG-UCC AGCTCAAGACTCTCGGTTTG GGAATTGTATATTCAATGGTTCGCT 944 1.000 47.5
trnG-UCC_p3 trnG-UCC CCCCCTGAAAAAGCTCAAGA GGAATTGTATATTCAATGGTTCGCT 955 1.000 47.4
trnG-UCC_p4 trnG-UCC CCCCCTGAAAAAGCTCAAGA GGAATTGTATATTCAATGGTTCGC 955 1.000 47.4
trnG-UCC_p5 trnG-UCC CCCCCTGAAAAAGCTCAAGA TGGGAATTGTATATTCAATGGTTCG 957 1.000 47.4
trnR-UCU_p1 trnR-UCU ACGAAAAATCGGAATGAACG AGCCTTTACTTGCTATCGAA 135 1.000 47.6
trnR-UCU_p2 trnR-UCU ACGAAAAATCGGAATGAACG AGCCTTTACTTGCTATCGAAA 135 1.000 47.6
trnR-UCU_p3 trnR-UCU ACGAAAAATCGGAATGAACG AAGCCTTTACTTGCTATCGA 136 1.000 47.5
trnR-UCU_p4 trnR-UCU ACGAAAAATCGGAATGAACG AAAGCCTTTACTTGCTATCGA 137 1.000 47.5
trnR-UCU_p5 trnR-UCU ACGAAAAATCGGAATGAACG AAGCCTTTACTTGCTATCGAA 136 1.000 47.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Euphrasia cisalpina PZ095197.1 144811 View on NCBI ↗
Euphrasia hirtella PZ095195.1 144829 View on NCBI ↗
Euphrasia picta PZ095196.1 118190 View on NCBI ↗