Markers + reference

Diplacus

8 species · Phrymaceae · Lamiales

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Species 8
Genome length 154–154 kb
Candidate markers 268
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 531 0.0098 0.98 58.8 yes View details
trnK-UUU-rps16 LSC 908 0.0059 0.97 59.0 yes View details
rps16-trnQ-UUG LSC 1210 0.0145 0.98 56.0 yes View details
trnT-GGU-psbD LSC 1340 0.0047 0.99 52.6 yes View details
ycf3-trnS-GGA LSC 628 0.0062 0.99 58.6 yes View details
ndhC-trnV-UAC LSC 922 0.0040 1.00 44.4 yes View details
ndhF SSC 2253 0.0040 1.00 43.1 yes View details
ycf1 SSC 5562 0.0038 1.00 45.6 yes View details
psaA-ycf3 LSC 756 0.0043 0.98 54.2 yes View details
petA-psbJ LSC 988 0.0038 1.00 52.1 yes View details
atpH-atpI LSC 994 0.0047 0.99 51.5 yes View details
rps2-rpoC2 LSC 218 0.0075 1.00 51.4 yes View details
accD LSC 1518 0.0026 1.00 51.3 yes View details
psbM-trnD-GUC LSC 525 0.0013 1.00 50.1 yes View details
trnC-GCA-petN LSC 669 0.0034 1.00 49.3 yes View details
psbB-psbT LSC 191 0.0026 1.00 49.3 yes View details
psbZ-trnG-GCC LSC 275 0.0071 1.00 49.0 yes View details
psaC-ndhE SSC 263 0.0054 0.95 49.0 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 95 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 TTCCCTCTAGACCTAGCTGC 597–656 1.000 82.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 611–670 1.000 82.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 610–669 1.000 82.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 612–671 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA TTTTGTTTTCTGCATGGGCG TTCCCTCTAGACCTAGCTGC 666–725 1.000 81.8
trnK-UUU_p1 trnK-UUU TTCGTGTCAACCAATCCCAA AGACTCTTTGTTGGAGGTTGA 2743–2751 1.000 60.4
trnK-UUU_p2 trnK-UUU TTCGTGTCAACCAATCCCAA ACTCTTTGTTGGAGGTTGAAGT 2741–2749 1.000 60.2
trnK-UUU_p3 trnK-UUU GTTCGTGTCAACCAATCCCA AGACTCTTTGTTGGAGGTTGA 2744–2752 1.000 60.0
trnK-UUU_p4 trnK-UUU TGTTCGTGTCAACCAATCCC AGACTCTTTGTTGGAGGTTGA 2745–2753 1.000 60.0
trnK-UUU_p5 trnK-UUU GTTCGTGTCAACCAATCCCA ACTCTTTGTTGGAGGTTGAAGT 2742–2750 1.000 59.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 1024–1070 1.000 68.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 1023–1069 1.000 68.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GTGCTCAACCCACAGGAAC 1038–1084 1.000 67.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCCACAGGAACT 1023–1069 1.000 67.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGGAACT 1022–1068 1.000 67.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1286–1315 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1269–1298 1.000 82.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1287–1316 1.000 81.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1284–1313 1.000 80.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1283–1312 1.000 80.5
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCTGCGG 1078–1079 1.000 79.6
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TCCTGTCATGTTCCTCGGAT 1126–1127 1.000 79.5
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCTGCGG 1096–1097 1.000 79.2
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TCCTGTCATGTTCCTCGGAT 1144–1145 1.000 79.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTGCAACTTTAGCTGCGG 1095–1096 1.000 78.7
rps2-rpoC2_p1 rps2-rpoC2 CCCAAAATGAACTCCTGCCT TTTGAGGGGGAAATGAGAGA 397–399 1.000 62.6
rps2-rpoC2_p2 rps2-rpoC2 CCCAAAATGAACTCCTGCCT TTGAGGGGGAAATGAGAGAT 396–398 1.000 60.7
rps2-rpoC2_p3 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TTTGAGGGGGAAATGAGAGA 380–382 1.000 60.6
rps2-rpoC2_p4 rps2-rpoC2 CCCAAAATGAACTCCTGCCT TTTGAGGGGGAAATGAGAGAT 397–399 1.000 59.3
rps2-rpoC2_p5 rps2-rpoC2 CCCAAAATGAACTCCTGCCT ATTTGAGGGGGAAATGAGAGA 398–400 1.000 59.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Diplacus aridus NC_068021.1 153622 View on NCBI ↗
Diplacus aurantiacus NC_068022.1 154022 View on NCBI ↗
Diplacus calycinus NC_068023.1 153775 View on NCBI ↗
Diplacus clevelandii NC_068024.1 153966 View on NCBI ↗
Diplacus grandiflorus NC_068025.1 153718 View on NCBI ↗
Diplacus longiflorus NC_068026.1 153726 View on NCBI ↗
Diplacus parviflorus NC_068028.1 154020 View on NCBI ↗
Diplacus puniceus NC_068027.1 153747 View on NCBI ↗