Markers + reference

Tacinga

2 species · Cactaceae · Caryophyllales

Back to catalogue

Species 2
Genome length 122–123 kb
Candidate markers 234
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 234 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 Genome 2188 0.4619 0.87 79.9 yes View details
ndhH Genome 1182 0.4794 0.88 81.8 yes View details
ndhA Genome 2187 0.4471 0.81 78.2 yes View details
ndhI Genome 516 0.4820 0.92 81.0 yes View details
ndhG Genome 531 0.4742 0.84 79.0 yes View details
ndhE Genome 306 0.4603 0.78 72.8 yes View details
ndhD Genome 1503 0.4827 0.84 80.6 yes View details
ccsA Genome 981 0.4736 0.73 77.6 yes View details
ndhE-psaC Genome 326 0.4557 0.94 77.5 yes View details
ndhA-ndhI Genome 132 0.4194 0.94 77.1 yes View details
rps15 Genome 267 0.4475 0.96 76.1 yes View details
ndhD-ccsA Genome 219 0.4495 0.90 76.1 yes View details
ndhI-ndhG Genome 367 0.4572 0.83 75.4 yes View details
ndhG-ndhE Genome 252 0.4977 0.88 75.4 yes View details
rpl32-ycf1 Genome 179 0.4101 0.99 73.1 yes View details
trnL-UAG-rpl32 Genome 109 0.4167 0.77 72.7 yes View details
ycf1-rps15 Genome 270 0.4714 0.78 72.6 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl32-ycf1_p1 rpl32-ycf1 AGTAAGGGGGCAATACCTGT GCCTACTCAATACTAGGCGC 1054 0.500 59.3
rpl32-ycf1_p2 rpl32-ycf1 GGGATATTGGGCAGCGTTAA GCCTACTCAATACTAGGCGC 544 0.500 59.3
rpl32-ycf1_p3 rpl32-ycf1 AGTAAGGGGGCAATACCTGT AAAACCAGTTGATGCGGCTA 987 0.500 59.1
rpl32-ycf1_p4 rpl32-ycf1 AGTAAGGGGGCAATACCTGT TAAAACCAGTTGATGCGGCT 988 0.500 59.1
rpl32-ycf1_p5 rpl32-ycf1 GGGATATTGGGCAGCGTTAA AAAACCAGTTGATGCGGCTA 477 0.500 59.0
ycf1_p1 ycf1 ACGAACAATAGAAGTCGGCC GCCATAGGTTTTCCCCGATT 2996 0.500 59.4
ycf1_p2 ycf1 TAGAAGTCGGCCTAACCCAA GCCATAGGTTTTCCCCGATT 2988 0.500 59.0
ycf1_p3 ycf1 GAAGTCGGCCTAACCCAAAA GCCATAGGTTTTCCCCGATT 2986 0.500 58.7
ycf1_p4 ycf1 ATAGAAGTCGGCCTAACCCA GCCATAGGTTTTCCCCGATT 2989 0.500 58.1
ycf1_p5 ycf1 ACGAACAATAGAAGTCGGCC ATTGGACGCTAAGACAAGGC 2407 0.500 57.9
ycf1-rps15_p1 ycf1-rps15 ACGGGCTCATAGGAGTAGAC GCCATAGGTTTTCCCCGATT 1062 0.500 59.3
ycf1-rps15_p2 ycf1-rps15 CACGGGCTCATAGGAGTAGA GCCATAGGTTTTCCCCGATT 1063 0.500 59.3
ycf1-rps15_p3 ycf1-rps15 CGGGCTCATAGGAGTAGACA GCCATAGGTTTTCCCCGATT 1061 0.500 59.3
ycf1-rps15_p4 ycf1-rps15 TCACGGGCTCATAGGAGTAG GCCATAGGTTTTCCCCGATT 1064 0.500 59.3
ycf1-rps15_p5 ycf1-rps15 ACCTAGACGTCGTCGAGAAT GCCATAGGTTTTCCCCGATT 966 0.500 59.3
rps15_p1 rps15 ACGGGCTCATAGGAGTAGAC GCCATAGGTTTTCCCCGATT 1062 0.500 59.3
rps15_p2 rps15 CACGGGCTCATAGGAGTAGA GCCATAGGTTTTCCCCGATT 1063 0.500 59.3
rps15_p3 rps15 CGGGCTCATAGGAGTAGACA GCCATAGGTTTTCCCCGATT 1061 0.500 59.3
rps15_p4 rps15 TCACGGGCTCATAGGAGTAG GCCATAGGTTTTCCCCGATT 1064 0.500 59.3
rps15_p5 rps15 ACCTAGACGTCGTCGAGAAT GCCATAGGTTTTCCCCGATT 966 0.500 59.3
ndhH_p1 ndhH GCCTTGTCTTAGCGTCCAAT CGTTGTTGTATACCTGCGGA 1969 0.500 57.9
ndhH_p2 ndhH GCCTTGTCTTAGCGTCCAAT TGACTGCTATAGAGGGTCCG 2106 0.500 57.8
ndhH_p3 ndhH GCCTTGTCTTAGCGTCCAAT TGAAGAATTCCCAAAGGGCC 2008 0.500 57.4
ndhH_p4 ndhH GCCTTGTCTTAGCGTCCAAT CCGTCTGCTAGAGCTTGAAG 2023 0.500 57.3
ndhH_p5 ndhH GGGGGTCCGTTGAATTTCAA CGTTGTTGTATACCTGCGGA 1697 0.500 57.0
ndhA_p1 ndhA GGTTTATCGGGACCAATGCT CGTACCGCTTGTTGACCATA 2901 0.500 59.6
ndhA_p2 ndhA TGGGAAGTCCAATGGCAAAA CGTACCGCTTGTTGACCATA 2814 0.500 59.2
ndhA_p3 ndhA TTCGTTCCCCGGGTTTTATC CGTACCGCTTGTTGACCATA 2492 0.500 59.1
ndhA_p4 ndhA AGTAAAAAGCCATCCCCTGC CGTACCGCTTGTTGACCATA 2619 0.500 58.8
ndhA_p5 ndhA GTAAAAAGCCATCCCCTGCT CGTACCGCTTGTTGACCATA 2618 0.500 58.8

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
Tacinga palmadora OQ613410.1 123381 View on NCBI ↗
Tacinga saxatilis NC_083959.1 121937 View on NCBI ↗