Markers + reference

Symphytum

2 species · Boraginaceae · Boraginales

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Species 2
Genome length 149–150 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1106 0.0109 0.99 54.1 yes View details
rps16-trnQ-UUG LSC 667 0.0180 1.00 58.8 yes View details
trnS-UGA-psbZ LSC 357 0.0252 1.00 68.2 yes View details
ndhC-trnV-UAC LSC 773 0.0142 1.00 63.8 yes View details
psbE-petL LSC 850 0.0118 0.70 51.1 yes View details
clpP LSC 1946 0.0082 1.00 53.2 yes View details
ycf1 IRb 1083 0.0065 0.99 61.8 no View details
rpl32-trnL-UAG SSC 228 0.0136 0.96 55.4 yes View details
ccsA SSC 972 0.0082 1.00 50.4 yes View details
rps15 SSC 264 0.0038 1.00 40.3 yes View details
rps15-ycf1 SSC 330 0.0301 0.91 73.7 yes View details
ycf1 SSC 5391 0.0123 1.00 58.3 yes View details
trnI-CAU-ycf2 IRb 139 0.0458 0.94 83.1 yes View details
ycf2-trnI-CAU IRa 139 0.0458 0.94 83.1 yes View details
psbI-trnS-GCU LSC 113 0.0442 1.00 76.1 yes View details
ccsA-ndhD SSC 173 0.0578 1.00 72.4 yes View details
rpoC1-rpoB LSC 32 0.0312 1.00 70.5 yes View details
rrn16-trnI-GAU IRb 289 0.0311 1.00 70.4 yes View details
trnI-GAU-rrn16 IRa 289 0.0311 1.00 70.4 yes View details
psaA-ycf3 LSC 731 0.0140 0.98 68.9 yes View details
atpI-rps2 LSC 198 0.0253 1.00 67.0 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
trnK-UUU_p1 trnK-UUU ACCTATCATTTCAATATGGCGG GGGGCCTATCTATTTTTCAT 2625–2642 1.000 41.1
trnK-UUU_p2 trnK-UUU ACCTATCATTTCAATATGGCGG GGGGCCTATCTATTTTTCATT 2625–2642 1.000 41.1
trnK-UUU_p3 trnK-UUU ACCTATCATTTCAATATGGCGG GGGGCCTATCTATTTTTCATTT 2625–2642 1.000 41.1
trnK-UUU_p4 trnK-UUU CCTATCATTTCAATATGGCGG GGGGCCTATCTATTTTTCAT 2624–2641 1.000 41.1
trnK-UUU_p5 trnK-UUU CCTATCATTTCAATATGGCGG GGGGCCTATCTATTTTTCATT 2624–2641 1.000 41.1
rps16_p1 rps16 CCCCCTTAATTTGTTTGTATTTCCT ATCAACTCCACACCCCTTCT 1173–1181 1.000 41.4
rps16_p2 rps16 CCCCCTTAATTTGTTTGTATTTCCT TTGAATCAACTCCACACCCC 1177–1185 1.000 41.4
rps16_p3 rps16 CCCCCTTAATTTGTTTGTATTTCCT TCAACTCCACACCCCTTCTA 1172–1180 1.000 41.4
rps16_p4 rps16 CCCCCTTAATTTGTTTGTATTTCC ATCAACTCCACACCCCTTCT 1173–1181 1.000 41.4
rps16_p5 rps16 CCCCCTTAATTTGTTTGTATTTCCT TGAATCAACTCCACACCCCT 1176–1184 1.000 41.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 752 1.000 80.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 740 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA TCTTGAATCGAAATGGGGCG 813 1.000 75.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA TTCGGAGGTTCGAATCCTTC 756 1.000 75.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCGTTCAAGTCGCA TAAGGCAACGGGTTTTGGTC 782 1.000 75.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TAAAGCGGCGGATTGCTAAT 205 1.000 74.2
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TAGGAGAGATGGCTGAGTGG 227 1.000 73.7
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TAAAGCGGCGGATTGCTAAT 205 1.000 71.8
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA CGAGTTATTCGTACCGAGGG 177 1.000 71.6
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TAGGAGAGATGGCTGAGTGG 227 1.000 71.3
atpI-rps2_p1 atpI-rps2 GGAAACCCCCTATTTGCCAA TTCCAGCAAATGATGACGCT 399 1.000 79.2
atpI-rps2_p2 atpI-rps2 GTTGACCTACTTCCACACCG TTCCAGCAAATGATGACGCT 372 1.000 78.0
atpI-rps2_p3 atpI-rps2 AAGTACTTGACCGTGGACCT TTCCAGCAAATGATGACGCT 419 1.000 77.3
atpI-rps2_p4 atpI-rps2 GGAAACCCCCTATTTGCCAA TGTGAAGGGCGTTCTAGCTA 334 1.000 77.2
atpI-rps2_p5 atpI-rps2 GGAAACCCCCTATTTGCCAA TTTGTGAAGGGCGTTCTAGC 336 1.000 76.9
rpoC1-rpoB_p1 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA CGGAGGATGCTCCAGAATCT 271 1.000 69.8
rpoC1-rpoB_p2 rpoC1-rpoB GCCCAAGCGCTTATTTGTTG CGGAGGATGCTCCAGAATCT 222 1.000 67.5
rpoC1-rpoB_p3 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA GGAGGATGCTCCAGAATCTT 270 1.000 66.9
rpoC1-rpoB_p4 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA GGAGGATGCTCCAGAATCTTT 270 1.000 64.8
rpoC1-rpoB_p5 rpoC1-rpoB CCCAAGCGCTTATTTGTTGA CGGAGGATGCTCCAGAATCT 221 1.000 64.7

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
Symphytum officinale PQ456197.1 149639 View on NCBI ↗
Symphytum tuberosum subsp. angustifolium PP024539.1 148914 View on NCBI ↗