Markers + reference

Salmonopuntia

2 species · Cactaceae · Caryophyllales

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Species 2
Genome length 147–148 kb
Candidate markers 264
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 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
rps12 Genome 788 0.0076 1.00 62.8 yes View details
rpl23 Genome 267 0.0112 1.00 44.3 yes View details
accD Genome 3429 0.0079 0.97 50.6 yes View details
rps18 Genome 423 0.0071 1.00 48.2 yes View details
ndhA-trnL-UAG Genome 819 0.0012 1.00 54.7 yes View details
trnV-GAC-rps12 Genome 1505 0.0040 1.00 55.8 no View details
atpA-atpF Genome 69 0.0580 1.00 82.2 yes View details
trnR-UCU-atpA Genome 101 0.0495 1.00 81.0 yes View details
rpoC1-rpoB Genome 26 0.0385 1.00 74.6 yes View details
trnL-UAG-ccsA Genome 114 0.0263 1.00 65.2 yes View details
trnR-ACG-trnN-GUU Genome 622 0.0000 0.96 62.5 yes View details
trnN-GUU-trnR-ACG Genome 622 0.0000 0.96 62.5 yes View details
petA-psbJ Genome 1041 0.0058 1.00 62.1 yes View details
accD-psaI Genome 621 0.0048 1.00 61.7 yes View details
rpl23-rpl2 Genome 66 0.0152 1.00 61.2 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps12_p1 rps12 TACGGTTCTGTAGAGTGGCA CAGTACCTCGACGTGACATG 909 1.000 79.0
rps12_p2 rps12 TACGGTTCTGTAGAGTGGCA TACAGTACCTCGACGTGACA 911 1.000 78.5
rps12_p3 rps12 TACGGTTCTGTAGAGTGGCA GTACCTCGACGTGACATGAG 907 1.000 78.4
rps12_p4 rps12 TACGGTTCTGTAGAGTGGCA AGTACCTCGACGTGACATGA 908 1.000 78.4
rps12_p5 rps12 ATTGAACGAGGAGCCGTATG CAGTACCTCGACGTGACATG 945 1.000 77.9
rpl23_p1 rpl23 GAATGGTTAAAGCGCCCAAC CGGTATAGACGCTTATGGCC 683 1.000 80.4
rpl23_p2 rpl23 GAATGGTTAAAGCGCCCAAC CTTAGATCCGGCTCTACCCA 1131 1.000 80.3
rpl23_p3 rpl23 GAATGGTTAAAGCGCCCAAC TTATGGCCTCCCCCTCTATG 671 1.000 80.2
rpl23_p4 rpl23 CCAAATTCGGGGGTCAAAGA CTTAGATCCGGCTCTACCCA 1472–1474 1.000 79.7
rpl23_p5 rpl23 TCCAAATTCGGGGGTCAAAG CTTAGATCCGGCTCTACCCA 1473–1475 1.000 79.7
rpl23-rpl2_p1 rpl23-rpl2 TCATTACGCTTCAATCGGGT TGCTCGGGGTAGAAGTTTTG 144 1.000 73.7
rpl23-rpl2_p2 rpl23-rpl2 TCATTACGCTTCAATCGGGT GCTCGGGGTAGAAGTTTTGT 143 1.000 73.6
rpl23-rpl2_p3 rpl23-rpl2 TCATTACGCTTCAATCGGGT GTGCTCGGGGTAGAAGTTTT 145 1.000 73.6
rpl23-rpl2_p4 rpl23-rpl2 TCATTACGCTTCAATCGGGT CAACGACGCTGTCCATAGAT 217 1.000 73.2
rpl23-rpl2_p5 rpl23-rpl2 TCATTACGCTTCAATCGGGT ATTGTCTACGGCTCCATTGC 167 1.000 72.4
trnG-UCC_p1 trnG-UCC TCGACAAAAGGTTCAGCTCA TGGATTGTACGCGAGATGAG 876 1.000 71.3
trnG-UCC_p2 trnG-UCC AGCTCGACAAAAGGTTCAGC TGGATTGTACGCGAGATGAG 879 1.000 70.0
trnG-UCC_p3 trnG-UCC GCTCGACAAAAGGTTCAGCT TGGATTGTACGCGAGATGAG 878 1.000 70.0
trnG-UCC_p4 trnG-UCC TCGACAAAAGGTTCAGCTCA GGATTGTACGCGAGATGAGA 875 1.000 69.0
trnG-UCC_p5 trnG-UCC GCTCGACAAAAGGTTCAGCT GGATTGTACGCGAGATGAGA 877 1.000 67.7
trnR-UCU-atpA_p1 trnR-UCU-atpA ATCGGAAAAGCGTCCATTGT GAGGAAGCAGAAGCCCTTTT 257 1.000 79.5
trnR-UCU-atpA_p2 trnR-UCU-atpA CGGAAAAGCGTCCATTGTCT GAGGAAGCAGAAGCCCTTTT 255 1.000 74.2
trnR-UCU-atpA_p3 trnR-UCU-atpA TCGGAAAAGCGTCCATTGTC GAGGAAGCAGAAGCCCTTTT 256 1.000 74.1
trnR-UCU-atpA_p4 trnR-UCU-atpA ATCGGAAAAGCGTCCATTGT TTACTGAGGAAGCAGAAGCC 262 1.000 73.9
trnR-UCU-atpA_p5 trnR-UCU-atpA AATCGGAAAAGCGTCCATTG GAGGAAGCAGAAGCCCTTTT 258 1.000 73.5
atpA-atpF_p1 atpA-atpF CAATGCCGTCACCTACTTGA GCATGTTTGGTGCCATGAAA 222 1.000 79.4
atpA-atpF_p2 atpA-atpF ATGCCGTCACCTACTTGAAG GCATGTTTGGTGCCATGAAA 220 1.000 77.0
atpA-atpF_p3 atpA-atpF TGCTAATTTCGTCTGCTCGA GCATGTTTGGTGCCATGAAA 135 1.000 75.9
atpA-atpF_p4 atpA-atpF AATGCCGTCACCTACTTGAA GCATGTTTGGTGCCATGAAA 221 1.000 73.3
atpA-atpF_p5 atpA-atpF TGCCGTCACCTACTTGAAGT GCATGTTTGGTGCCATGAAA 219 1.000 72.5

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
Salmonopuntia salmiana NC_083957.1 147474 View on NCBI ↗
Salmonopuntia schickendantzii NC_083958.1 148035 View on NCBI ↗