Markers + reference

Baptisia

2 species · Fabaceae · Fabales

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Species 2
Genome length 152–152 kb
Candidate markers 262
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnC-GCA-rpoB LSC 685 0.0015 1.00 46.6 yes View details
rpoC1 LSC 2833 0.0007 1.00 56.4 yes View details
atpI-atpH LSC 687 0.0029 1.00 60.4 yes View details
trnT-UGU-trnL-UAA LSC 1077 0.0010 0.97 62.6 yes View details
trnQ-UUG-accD LSC 1834 0.0016 1.00 59.0 yes View details
petA-psbJ LSC 1187 0.0068 1.00 62.9 yes View details
petD LSC 1199 0.0017 1.00 59.8 yes View details
rps8 LSC 405 0.0025 1.00 42.7 yes View details
rpl16 LSC 1521 0.0013 1.00 59.5 yes View details
ndhD SSC 1500 0.0013 1.00 55.5 yes View details
ndhA SSC 2253 0.0018 1.00 48.8 yes View details
petN-psbM LSC 1326 0.0008 0.98 61.2 yes View details
petB LSC 1408 0.0007 1.00 59.2 yes View details
rbcL-atpB LSC 769 0.0000 1.00 59.1 yes View details
psbK-trnQ-UUG LSC 553 0.0018 1.00 59.0 yes View details
trnG-UCC-trnS-GCU LSC 756 0.0000 1.00 58.9 yes View details
atpF LSC 1354 0.0000 1.00 58.8 yes View details
trnT-GGU-psbD LSC 1435 0.0000 1.00 58.8 yes View details
clpP LSC 2009 0.0000 1.00 57.8 yes View details
ndhF SSC 2304 0.0004 1.00 57.3 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rbcL-atpB_p1 rbcL-atpB AACACCAGCTTTGAACCCAA CCTGGGGGAAAAGCTACATC 930–933 1.000 78.7
rbcL-atpB_p2 rbcL-atpB AACACCAGCTTTGAACCCAA CTGGGGGAAAAGCTACATCC 929–932 1.000 78.7
rbcL-atpB_p3 rbcL-atpB AACACCAGCTTTGAACCCAA GGGGGAAAAGCTACATCCAG 927–930 1.000 78.7
rbcL-atpB_p4 rbcL-atpB AACACCAGCTTTGAACCCAA AAGCTACATCCAGTACCGGA 920–923 1.000 77.9
rbcL-atpB_p5 rbcL-atpB AACACCAGCTTTGAACCCAA CTACATCCAGTACCGGACCA 917–920 1.000 77.3
trnV-UAC_p1 trnV-UAC TCAAAGAGGTTGGATGATGT AGTATAGAGTATTTAGTAATGAGAGA 818–819 1.000 40.1
trnV-UAC_p2 trnV-UAC CAATCAAAGAGGTTGGATGATGT AGTATAGAGTATTTAGTAATGAGAGA 821–822 1.000 40.1
trnV-UAC_p3 trnV-UAC ATCAAAGAGGTTGGATGATGT AGTATAGAGTATTTAGTAATGAGAGA 819–820 1.000 40.1
trnV-UAC_p4 trnV-UAC TCAATCAAAGAGGTTGGATGATG AGTATAGAGTATTTAGTAATGAGAGA 822–823 1.000 40.1
trnV-UAC_p5 trnV-UAC TCAATCAAAGAGGTTGGATGA AGTATAGAGTATTTAGTAATGAGAGA 822–823 1.000 40.1
trnC-GCA-rpoB_p1 trnC-GCA-rpoB CTCTTGTTGATCAGGCGACA ATTTCCTCATTTCCACCCCC 794 1.000 75.0
trnC-GCA-rpoB_p2 trnC-GCA-rpoB TCTTGTTGATCAGGCGACAC ATTTCCTCATTTCCACCCCC 793 1.000 74.1
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAAGGATTTGCAGTCCCCC ATTTCCTCATTTCCACCCCC 755 1.000 72.9
trnC-GCA-rpoB_p4 trnC-GCA-rpoB TCTCTTGTTGATCAGGCGAC ATTTCCTCATTTCCACCCCC 795 1.000 72.7
trnC-GCA-rpoB_p5 trnC-GCA-rpoB CTCTTGTTGATCAGGCGACA TTCCTCATTTCCACCCCCAA 792 1.000 72.7
rpoC1_p1 rpoC1 ACGATCTTTGGCTCTGGAAC AAGACCTGAATTCACACCGG 2980–2981 1.000 77.8
rpoC1_p2 rpoC1 ACGATCTTTGGCTCTGGAAC CAACCGGGAAGACCTGAATT 2988–2989 1.000 77.7
rpoC1_p3 rpoC1 ACGATCTTTGGCTCTGGAAC CCGGGAAGACCTGAATTCAC 2985–2986 1.000 77.2
rpoC1_p4 rpoC1 ACGATCTTTGGCTCTGGAAC CGGGAAGACCTGAATTCACA 2984–2985 1.000 75.5
rpoC1_p5 rpoC1 CGATCTTTGGCTCTGGAACT AAGACCTGAATTCACACCGG 2979–2980 1.000 75.5
atpI-atpH_p1 atpI-atpH GCTGCGGCTTATATAGGTGA CGCAATCCCTTCTACAGCTT 849–851 1.000 74.0
atpI-atpH_p2 atpI-atpH GCTGCGGCTTATATAGGTGA ATAACGGAAGCGGCAGAAAT 761–763 1.000 74.0
atpI-atpH_p3 atpI-atpH ACAAGCGGTATTCAAGCTCT CGCAATCCCTTCTACAGCTT 885–887 1.000 73.8
atpI-atpH_p4 atpI-atpH ACAAGCGGTATTCAAGCTCT ATAACGGAAGCGGCAGAAAT 797–799 1.000 73.7
atpI-atpH_p5 atpI-atpH GCTGCGGCTTATATAGGTGA AATAACGGAAGCGGCAGAAA 762–764 1.000 72.8
atpF_p1 atpF TGCGAATCCTTTTGTTTAATCCT TGCACGAATGGTTACCATGA 1548 1.000 44.4
atpF_p2 atpF TGCGAATCCTTTTGTTTAATCCT ATCTGCACGAATGGTTACCA 1551 1.000 42.0
atpF_p3 atpF TGCGAATCCTTTTGTTTAATCCT CTGCACGAATGGTTACCATG 1549 1.000 41.6
atpF_p4 atpF TTGCGAATCCTTTTGTTTAATCCT TGCACGAATGGTTACCATGA 1549 1.000 41.5
atpF_p5 atpF TGCGAATCCTTTTGTTTAATCC TGCACGAATGGTTACCATGA 1548 1.000 41.1

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
Baptisia australis PV870838.1 151555 View on NCBI ↗
Baptisia leucophaea NC_067521.1 151574 View on NCBI ↗