Markers + reference

Coursetia

2 species · Fabaceae · Fabales

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Species 2
Genome length 157–157 kb
Candidate markers 264
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5334 0.4184 0.88 75.7 yes View details
ndhH SSC 1182 0.4701 0.78 78.9 yes View details
ndhA SSC 2317 0.4667 0.84 78.9 yes View details
ndhI SSC 486 0.4665 0.83 77.8 yes View details
psaC SSC 246 0.4821 0.79 72.9 yes View details
ndhD SSC 1497 0.4652 0.82 80.1 yes View details
ndhF SSC 2244 0.4488 0.87 80.0 yes View details
trnE-UUC-trnT-GGU LSC 804 0.3179 0.94 83.3 yes View details
trnL-UAG-rpl32 SSC 592 0.4266 0.84 80.3 yes View details
ndhG SSC 531 0.4472 0.84 79.1 yes View details
rpl32-ndhF SSC 711 0.4069 0.78 78.8 yes View details
ndhI-ndhG SSC 467 0.4582 0.85 78.0 yes View details
trnY-GUA-trnE-UUC LSC 60 0.4545 0.92 77.5 yes View details
trnD-GUC-trnY-GUA LSC 468 0.4375 0.82 77.3 yes View details
ndhE SSC 306 0.4296 0.93 76.9 yes View details
trnD-GUC LSC 74 0.4789 0.96 76.4 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnD-GUC_p1 trnD-GUC TCTTCGTCGGAACCTTTACC AAGTATGCCCCCATCGTCTA 898 0.500 53.4
trnD-GUC_p2 trnD-GUC TCTTCGTCGGAACCTTTACC CGGCCCAAAAATTTGCTGAT 682 0.500 53.4
trnD-GUC_p3 trnD-GUC CTTCGTCGGAACCTTTACCT AAGTATGCCCCCATCGTCTA 897 0.500 53.3
trnD-GUC_p4 trnD-GUC CTTCGTCGGAACCTTTACCT CGGCCCAAAAATTTGCTGAT 681 0.500 53.3
trnD-GUC_p5 trnD-GUC TCTTCGTCGGAACCTTTACC TTGTTCTCCCAACATGACGG 615 0.500 53.3
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GTATTCATCGGGACTGACGG ACATCTACCCACCCATTCCA 1288 0.500 58.8
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GTATTCATCGGGACTGACGG AAGTATGCCCCCATCGTCTA 773 0.500 58.1
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GTATTCATCGGGACTGACGG ATGGATTCTTCCTGGGTCGA 647 0.500 58.0
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GTATTCATCGGGACTGACGG TGGATTCTTCCTGGGTCGAT 646 0.500 58.0
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GTATTCATCGGGACTGACGG TCTCTTTCAAGGAGGCAACG 738 0.500 57.6
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC ATCAGCAAATTTTTGGGCCG ACATCTACCCACCCATTCCA 751 0.500 59.1
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC CCGTCATGTTGGGAGAACAA ACATCTACCCACCCATTCCA 818 0.500 59.0
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC GTATTCATCGGGACTGACGG ACATCTACCCACCCATTCCA 1288 0.500 58.8
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC ATCAGCAAATTTTTGGGCCG AAGTATGCCCCCATCGTCTA 236 0.500 58.4
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC CCGTCATGTTGGGAGAACAA AAGTATGCCCCCATCGTCTA 303 0.500 58.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU ATCAGCAAATTTTTGGGCCG GAACCGATGACTTACGCCTT 1089 0.500 59.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU ATCAGCAAATTTTTGGGCCG CATCGGAAATATCGGCGGAT 1566 0.500 59.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CCGTCATGTTGGGAGAACAA GAACCGATGACTTACGCCTT 1156 0.500 59.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CCGTCATGTTGGGAGAACAA CATCGGAAATATCGGCGGAT 1633 0.500 59.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU ATCAGCAAATTTTTGGGCCG CCATGGCGTTACTCTACCAC 1068 0.500 58.7
ycf1_p1 ycf1 AGTAAAAGCAGCATACGCGA CTAGACAGGCGAACAGGTTC 423 0.500 59.9
ycf1_p2 ycf1 CAGTAAAAGCAGCATACGCG CTAGACAGGCGAACAGGTTC 424 0.500 59.4
ycf1_p3 ycf1 AGTAAAAGCAGCATACGCGA TTACCGAATTTTCAAGCGCG 928 0.500 58.1
ycf1_p4 ycf1 CAGTAAAAGCAGCATACGCG TTACCGAATTTTCAAGCGCG 929 0.500 57.5
ycf1_p5 ycf1 GTAAAAGCAGCATACGCGAG CTAGACAGGCGAACAGGTTC 422 0.500 57.2
ndhH_p1 ndhH AAAAAGGAGGGGGAGAGGAA CCGTCTGCTAGAGCTTGAAG 1836 0.500 58.2
ndhH_p2 ndhH AAAAGGAGGGGGAGAGGAAA CCGTCTGCTAGAGCTTGAAG 1835 0.500 58.2
ndhH_p3 ndhH AAAAAGGAGGGGGAGAGGAA TTTGTTCCGTCTGCTAGAGC 1842 0.500 58.2
ndhH_p4 ndhH AAAAGGAGGGGGAGAGGAAA TTTGTTCCGTCTGCTAGAGC 1841 0.500 58.2
ndhH_p5 ndhH AAAAGGAGGGGGAGAGGAAA TCAGGTCCAATACGCTGTTG 1793 0.500 58.1

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
Coursetia caatingicola PV870756.1 156717 View on NCBI ↗
Coursetia rostrata NC_067544.1 156835 View on NCBI ↗