Markers + reference

Verbascum

5 species · Scrophulariaceae · Lamiales

Back to catalogue

Species 5
Genome length 153–154 kb
Candidate markers 270
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1083 0.0066 1.00 58.7 yes View details
psaA-ycf3 LSC 813 0.0058 0.99 65.7 yes View details
ycf4-cemA LSC 660 0.0085 1.00 57.5 yes View details
ycf1 IRb 846 0.0005 1.00 44.1 no View details
rpl32-trnL-UAG SSC 884 0.0089 0.98 69.0 yes View details
ndhD SSC 1503 0.0020 1.00 33.7 yes View details
rps15-ycf1 SSC 427 0.0078 0.92 42.3 yes View details
ycf1 SSC 5385 0.0034 0.99 45.7 yes View details
ndhD-psaC SSC 124 0.0468 1.00 68.6 yes View details
rps2-rpoC2 LSC 220 0.0162 0.99 66.2 yes View details
atpH-atpI LSC 1049 0.0043 0.98 64.5 yes View details
trnV-GAC-rps12 IRa 1680 0.0010 0.99 62.1 yes View details
rps12-trnV-GAC IRb 1680 0.0017 0.98 61.9 yes View details
petN-psbM LSC 938 0.0038 1.00 61.7 yes View details
accD-psaI LSC 459 0.0052 1.00 61.6 yes View details
atpF LSC 1265 0.0030 1.00 61.2 yes View details
rpl16 LSC 1286 0.0031 1.00 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU ACTCCCAAGCACACGAAATT GCTCGATGGTTTGATTAACTCG 2855–2862 1.000 63.2
trnK-UUU_p2 trnK-UUU TAAAGACGGTTTTCGGTGCT GCTCGATGGTTTGATTAACTCG 2972–2979 1.000 61.4
trnK-UUU_p3 trnK-UUU GTAAAGACGGTTTTCGGTGC GCTCGATGGTTTGATTAACTCG 2973–2980 1.000 60.9
trnK-UUU_p4 trnK-UUU GACTCCCAAGCACACGAAAT GCTCGATGGTTTGATTAACTCG 2856–2863 1.000 59.6
trnK-UUU_p5 trnK-UUU CGTGTCAACCAATGCCACTA GCTCGATGGTTTGATTAACTCG 2773–2780 1.000 59.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 1214–1243 1.000 82.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1156–1185 1.000 82.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1197–1226 1.000 82.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1139–1168 1.000 81.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 1215–1244 1.000 81.4
atpF_p1 atpF TTTCATCGGCTCGAATGGTT AGAGGGGCAAAGTGATAGAA 1409–1415 1.000 62.5
atpF_p2 atpF TTTCATCGGCTCGAATGGTT AAGAGGGGCAAAGTGATAGA 1410–1416 1.000 62.4
atpF_p3 atpF TCATCGGCTCGAATGGTTAC AAGAGGGGCAAAGTGATAGA 1408–1414 1.000 61.6
atpF_p4 atpF TCATCGGCTCGAATGGTTAC AGAGGGGCAAAGTGATAGAA 1407–1413 1.000 61.6
atpF_p5 atpF TTTCATCGGCTCGAATGGTT AGAGGGGCAAAGTGATAGAAA 1409–1415 1.000 60.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCCTGTCATGTTCCTTGGA 1159–1185 1.000 80.2
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TCCCTGTCATGTTCCTTGGA 1160–1186 1.000 79.1
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1174–1200 1.000 78.8
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1169–1195 1.000 78.4
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1111–1137 1.000 78.3
rps2-rpoC2_p1 rps2-rpoC2 GCCTCCAGCATTTCTTCCAA TTCGAGGGGGAAATAAGAGA 380–384 1.000 56.8
rps2-rpoC2_p2 rps2-rpoC2 AAATGAACTCCTGCCTCCAG TTCGAGGGGGAAATAAGAGA 392–396 1.000 56.3
rps2-rpoC2_p3 rps2-rpoC2 TTGCGGAGATATAAGGTGCC TTCGAGGGGGAAATAAGAGA 445–449 1.000 55.7
rps2-rpoC2_p4 rps2-rpoC2 TGCGGAGATATAAGGTGCCA TTCGAGGGGGAAATAAGAGA 444–448 1.000 55.4
rps2-rpoC2_p5 rps2-rpoC2 CCATGGCCAAAATGAACTCC TTCGAGGGGGAAATAAGAGA 401–405 1.000 54.9
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TGCTACTGCGCTATTCATTCT 1048–1055 1.000 69.0
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TGCTACTGCGCTATTCATTCT 1046–1053 1.000 69.0
petN-psbM_p3 petN-psbM CGTAGTGTGGGGAAGAAGTG TGCTACTGCGCTATTCATTCT 1045–1052 1.000 68.4
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGCTATTCATTCT 1100–1107 1.000 67.8
petN-psbM_p5 petN-psbM GTAGTGTGGGGAAGAAGTGG TGCTACTGCGCTATTCATTCT 1044–1051 1.000 65.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Verbascum alpinum PP622707.1 153552 View on NCBI ↗
Verbascum chinense NC_051533.1 153618 View on NCBI ↗
Verbascum lychnitis PP622709.1 153392 View on NCBI ↗
Verbascum sinaiticum NC_064358.1 153481 View on NCBI ↗
Verbascum thapsus NC_053691.1 153338 View on NCBI ↗