Markers + reference

Penstemon

3 species · Plantaginaceae · Lamiales

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Species 3
Genome length 153–153 kb
Candidate markers 274
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 1266 0.0053 1.00 49.0 yes View details
atpH-atpI LSC 981 0.0144 0.99 59.6 yes View details
ndhF-rpl32 SSC 533 0.0176 1.00 57.7 yes View details
ndhG-ndhI SSC 366 0.0323 0.99 66.7 yes View details
ycf1-fragment SSC 5565 0.0129 1.00 53.8 yes View details
trnH-GUG-psbA LSC 246 0.0612 0.89 72.6 yes View details
trnK-UUU-rps16 LSC 678 0.0181 0.98 63.5 yes View details
rps16 LSC 1181 0.0100 0.99 51.8 yes View details
psbK-psbI LSC 400 0.0368 0.97 68.2 yes View details
trnG-GCC-trnM-CAU LSC 169 0.0454 1.00 77.3 yes View details
rps19-rpl2 IRb 63 0.0328 0.97 76.1 yes View details
ndhD-psaC SSC 81 0.0542 0.99 71.8 yes View details
trnR-UCU-atpA LSC 104 0.0128 1.00 71.2 no View details
psbT-psbN LSC 67 0.0498 1.00 68.0 yes View details
rps19 IRa 49 0.0620 0.90 66.5 yes View details
trnT-UGU-trnL-UAA LSC 671 0.0119 1.00 64.7 yes View details
rpl2-rps19 IRa 63 0.0328 0.97 64.0 yes View details
psbH-petB LSC 1005 0.0097 1.00 63.4 yes View details
rps16-trnQ-UUG LSC 840 0.0188 0.99 63.3 yes View details
rps19 LSC 279 0.0024 1.00 26.7 no 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
atpF_p1 atpF CAATACCATCGCCCACTTGA GCTGTAGAAGGTATCGCGAG 1960–1964 1.000 80.9
atpF_p2 atpF CACCCGCCATTACTTCATCA GCTGTAGAAGGTATCGCGAG 1996–2000 1.000 80.9
atpF_p3 atpF CCGTTTCGGCTACCACAATA GCTGTAGAAGGTATCGCGAG 2527–2531 1.000 80.8
atpF_p4 atpF ATTCGACTAATTCACCCGCC GCTGTAGAAGGTATCGCGAG 2008–2012 1.000 80.8
atpF_p5 atpF CCGTTTCGGCTACCACAATA GCCTTGGACTTGTCATTTGC 2339–2343 1.000 80.7
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1110–1115 1.000 79.1
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1127–1132 1.000 78.2
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1122–1127 1.000 77.8
atpH-atpI_p4 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1062–1067 1.000 77.1
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA TCCCTGTCATGTTCCTTGGA 1123–1128 1.000 76.6
trnG-GCC-trnM-CAU_p1 trnG-GCC-trnM-CAU AGAAGATGCGGGTTCGATTC CTTGAGGTCACGGGTTCAAA 236–240 1.000 82.9
trnG-GCC-trnM-CAU_p2 trnG-GCC-trnM-CAU AGAAGATGCGGGTTCGATTC TTACTTCTTCTCTTCGGCGC 293–297 1.000 82.5
trnG-GCC-trnM-CAU_p3 trnG-GCC-trnM-CAU AGAAGATGCGGGTTCGATTC GGGTAGAGCAGTTTGGTAGC 272–276 1.000 82.5
trnG-GCC-trnM-CAU_p4 trnG-GCC-trnM-CAU GAGAAGATGCGGGTTCGATT GGGTAGAGCAGTTTGGTAGC 273–277 1.000 82.5
trnG-GCC-trnM-CAU_p5 trnG-GCC-trnM-CAU GAGAAGATGCGGGTTCGATT TTACTTCTTCTCTTCGGCGC 294–298 1.000 82.4
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 733–750 1.000 78.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TCATTCCGGGGTTTCTCTGA 807–824 1.000 77.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 765–782 1.000 77.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 727–744 1.000 77.5
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TCATTCCGGGGTTTCTCTGA 839–856 1.000 76.9
psbT-psbN_p1 psbT-psbN CGAGAACCACCTAAAGTTCCA GATCCATTCGAGGAACACGG 133 1.000 68.4
psbT-psbN_p2 psbT-psbN CGAGAACCACCTAAAGTTCCA AGATCCATTCGAGGAACACG 134 1.000 67.1
psbT-psbN_p3 psbT-psbN TCGAGAACCACCTAAAGTTCC GATCCATTCGAGGAACACGG 134 1.000 66.2
psbT-psbN_p4 psbT-psbN TCGAGAACCACCTAAAGTTCC AGATCCATTCGAGGAACACG 135 1.000 64.9
psbT-psbN_p5 psbT-psbN TTCGAGAACCACCTAAAGTTCC GATCCATTCGAGGAACACGG 135 1.000 63.5
psbH-petB_p1 psbH-petB GTCGCAATGGCTCTATTTGC ATACTTGCCGACCATCGATG 1201–1211 1.000 79.5
psbH-petB_p2 psbH-petB GTCGCAATGGCTCTATTTGC ATCATACTTGCCGACCATCG 1204–1214 1.000 79.5
psbH-petB_p3 psbH-petB GTCGCAATGGCTCTATTTGC CATACTTGCCGACCATCGAT 1202–1212 1.000 79.5
psbH-petB_p4 psbH-petB AACTCCTTTGATGGGTGTCG ATACTTGCCGACCATCGATG 1217–1227 1.000 78.9
psbH-petB_p5 psbH-petB AACTCCTTTGATGGGTGTCG CATACTTGCCGACCATCGAT 1218–1228 1.000 78.9

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
Penstemon fruticosus NC_061025.1 152704 View on NCBI ↗
Penstemon personatus NC_061960.1 152602 View on NCBI ↗
Penstemon rostriflorus NC_061961.1 152598 View on NCBI ↗