Markers + reference

Chaenorhinum

2 species · Plantaginaceae · Lamiales

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Species 2
Genome length 151–151 kb
Candidate markers 269
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0000 1.00 29.7 yes View details
rps16-trnQ-UUG LSC 685 0.0029 1.00 60.4 yes View details
psbK-psbI LSC 386 0.0104 1.00 60.3 yes View details
ycf3-trnS-GGA LSC 809 0.0025 1.00 60.2 yes View details
ndhC-trnV-UAC LSC 1118 0.0027 0.99 60.9 yes View details
accD-psaI LSC 343 0.0058 1.00 56.7 yes View details
ycf4-cemA LSC 612 0.0033 1.00 60.6 yes View details
petA-psbJ LSC 1026 0.0029 1.00 60.5 yes View details
psbB LSC 1527 0.0007 1.00 47.3 yes View details
psbB-psbT LSC 168 0.0119 1.00 59.3 yes View details
rpl16 LSC 1283 0.0016 1.00 59.6 yes View details
ycf1 IRb 759 0.0026 1.00 60.3 yes View details
ycf1 SSC 972 0.0010 1.00 47.2 no View details
ycf1 SSC 5415 0.0006 1.00 51.8 no View details
psbF-psbE LSC 14 0.0714 1.00 83.9 yes View details
trnH-GUG-psbA LSC 238 0.0424 0.99 77.6 yes View details
rpl2-trnH-GUG IRa 57 0.0000 1.00 71.2 no View details
psaA-ycf3 LSC 729 0.0000 0.99 59.9 yes View details
rpl20-rps12 LSC 830 0.0012 1.00 59.8 yes View details
trnS-GCU-trnG-UCC LSC 671 0.0015 1.00 59.6 yes View details
atpH-atpI LSC 1001 0.0010 1.00 59.4 yes View details
psbD LSC 1062 0.0009 1.00 59.3 yes View details
petA LSC 963 0.0010 1.00 59.3 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 100 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 CAACCGTGCTAACCTTGGTA 356 1.000 80.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 358 1.000 80.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 370 1.000 80.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 369 1.000 80.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 371 1.000 80.1
psbA_p1 psbA TTGCTCCTTTATTTTCCCGA AAATTTCCGTGCTTGGGAGT 1168 1.000 55.5
psbA_p2 psbA TTGCTCCTTTATTTTCCCGA GTGCTTGGGAGTCTCTGATG 1160 1.000 55.3
psbA_p3 psbA TTGCTCCTTTATTTTCCCGA TGCTTGGGAGTCTCTGATGA 1159 1.000 55.1
psbA_p4 psbA TGCTCCTTTATTTTCCCGATTCT AAATTTCCGTGCTTGGGAGT 1167 1.000 54.8
psbA_p5 psbA TGCTCCTTTATTTTCCCGATTCT GTGCTTGGGAGTCTCTGATG 1159 1.000 54.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 775 1.000 79.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG CGAAATTGAAATGGGGCGTC 834 1.000 78.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTCG 833 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 758 1.000 78.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTCG 816 1.000 78.3
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT CGCCCTGGATCATTGGATAG 510 1.000 79.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG CGCCCTGGATCATTGGATAG 505 1.000 79.3
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT ATTACGCCCTGGATCATTGG 514 1.000 78.0
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG ATTACGCCCTGGATCATTGG 509 1.000 78.0
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT CGCCCTGGATCATTGGATAG 502 1.000 77.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACCACTAAACTATACCCGCT 726 1.000 61.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACCACTAAACTATACCCGCT 725 1.000 61.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACCACTAAACTATACCCGCT 780 1.000 60.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC ACCACTAAACTATACCCGCT 728 1.000 58.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGACGCTTTAGTCCACTCAG ACCACTAAACTATACCCGCT 721 1.000 58.2
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCCGCAG 1086 1.000 78.3
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TTTTGCAACTTTAGCCGCAG 1171 1.000 78.0
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TTTTGCAACTTTAGCCGCAG 1175 1.000 77.9
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 1104 1.000 77.9
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTGCAACTTTAGCCGCAG 1103 1.000 77.4

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
Chaenorhinum minus PP484624.1 151436 View on NCBI ↗
Chaenorhinum minus subsp. minus PP328793.1 151423 View on NCBI ↗