Markers + reference

Mammillaria

2 species · Cactaceae · Caryophyllales

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Species 2
Genome length 116–116 kb
Candidate markers 240
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 240 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaC SSC 246 0.0000 1.00 25.1 yes View details
rrn5-rrn4.5 SSC 780 0.2611 0.84 92.9 yes View details
ndhB-ycf2 SSC 278 0.0540 1.00 67.6 yes View details
psaC-ndhD SSC 152 0.1056 0.93 91.7 yes View details
rpoA-rps11 LSC 71 0.0423 1.00 76.3 yes View details
trnI-GAU SSC 35 0.0857 1.00 75.8 yes View details
trnN-GUU-trnR-ACG SSC 157 0.0338 0.94 67.5 yes View details
trnL-UAG-rpl32 SSC 1002 0.0080 1.00 63.3 yes View details
rps18 LSC 378 0.0132 1.00 61.7 yes View details
petB-petD LSC 980 0.0051 1.00 61.7 yes View details
rpl16-rps3 LSC 1029 0.0049 1.00 61.6 yes View details
atpH-atpI LSC 490 0.0082 1.00 61.2 yes View details
trnV-GAC-rps12 SSC 748 0.0040 1.00 61.1 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps18_p1 rps18 CCAGTTGAAGAACCCAAGCA TGAAAACAAACCAGCAATCCA 487 1.000 60.9
rps18_p2 rps18 CCCCAGTTGAAGAACCCAAG TGAAAACAAACCAGCAATCCA 489 1.000 60.3
rps18_p3 rps18 TGAAGAACCCAAGCAAGAGC TGAAAACAAACCAGCAATCCA 482 1.000 60.3
rps18_p4 rps18 CCAGTTGAAGAACCCAAGCA TTGAAAACAAACCAGCAATCCA 488 1.000 58.5
rps18_p5 rps18 CCCCAGTTGAAGAACCCAAG TTGAAAACAAACCAGCAATCCA 490 1.000 58.0
petB-petD_p1 petB-petD TGCCTCTTCTTACTGCCGTA ACCCATCCCTTTTGCCAATT 1153–1157 1.000 76.4
petB-petD_p2 petB-petD CTTGCCTCTTCTTACTGCCG ACCCATCCCTTTTGCCAATT 1155–1159 1.000 74.9
petB-petD_p3 petB-petD TCTTGCCTCTTCTTACTGCC ACCCATCCCTTTTGCCAATT 1156–1160 1.000 73.8
petB-petD_p4 petB-petD TGCCTCTTCTTACTGCCGTA CCCTTTTGCCAATTTAGCCC 1147–1151 1.000 73.6
petB-petD_p5 petB-petD TGCCTCTTCTTACTGCCGTA GACCCATCCCTTTTGCCAAT 1154–1158 1.000 73.3
rpoA-rps11_p1 rpoA-rps11 TTCAACACACTTCCACTGCA CGGAAGGGATGGAGCATTAC 246 1.000 79.1
rpoA-rps11_p2 rpoA-rps11 TTCAACACACTTCCACTGCA GAAGGGATGGAGCATTACGG 244 1.000 79.1
rpoA-rps11_p3 rpoA-rps11 TTCAACACACTTCCACTGCA GGAAGGGATGGAGCATTACG 245 1.000 79.1
rpoA-rps11_p4 rpoA-rps11 GGAGAGAGAATAAAGCGCCC GAAGGGATGGAGCATTACGG 294 1.000 78.9
rpoA-rps11_p5 rpoA-rps11 GGAGAGAGAATAAAGCGCCC GGAAGGGATGGAGCATTACG 295 1.000 78.9
rpl16-rps3_p1 rpl16-rps3 GTTCAAGTGCCTGAAGAGCA TATTGCGCCTATACGGTTCG 1222 1.000 76.7
rpl16-rps3_p2 rpl16-rps3 GTTCAAGTGCCTGAAGAGCA AAACCATTCGCGCGAAAATT 1245 1.000 76.7
rpl16-rps3_p3 rpl16-rps3 GTTCAAGTGCCTGAAGAGCA TTCCCCTACAAACCATTCGC 1254 1.000 75.8
rpl16-rps3_p4 rpl16-rps3 GTTCAAGTGCCTGAAGAGCA CCATTCGCGCGAAAATTGAT 1242 1.000 75.8
rpl16-rps3_p5 rpl16-rps3 AGGTTCAAGTGCCTGAAGAG TATTGCGCCTATACGGTTCG 1224 1.000 75.5
psaC_p1 psaC TCGTCTGGTATTTGAATATGTGGT GGTACGGGTTTTTGTCGGTA 411–420 1.000 48.5
psaC_p2 psaC CTGGTAAATCATTGATTCGTCTGG GGTACGGGTTTTTGTCGGTA 427–436 1.000 48.1
psaC_p3 psaC TGGTAAATCATTGATTCGTCTGG GGTACGGGTTTTTGTCGGTA 426–435 1.000 48.0
psaC_p4 psaC GGTAAATCATTGATTCGTCTGGT GGTACGGGTTTTTGTCGGTA 425–434 1.000 48.0
psaC_p5 psaC CGTCTGGTATTTGAATATGTGGT GGTACGGGTTTTTGTCGGTA 410–419 1.000 46.1
psaC-ndhD_p1 psaC-ndhD TTTAGGGCCTGAAACAACCC AGAACCTGCAAATATGGGCA 242–252 1.000 83.8
psaC-ndhD_p2 psaC-ndhD CCGGAGTATGGGTCTAGCTT AGAACCTGCAAATATGGGCA 224–234 1.000 82.1
psaC-ndhD_p3 psaC-ndhD TGTGAATCTGCCTGTCCAAC AGAACCTGCAAATATGGGCA 286–296 1.000 81.8
psaC-ndhD_p4 psaC-ndhD TGCCTGTCCAACCGATTTTT AGAACCTGCAAATATGGGCA 278–288 1.000 80.4
psaC-ndhD_p5 psaC-ndhD CAGAGGACTGTGTTGGTTGT AGAACCTGCAAATATGGGCA 312–322 1.000 79.4

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
Mammillaria crucigera MN517613.1 115505 View on NCBI ↗
Mammillaria huitzilopochtli MN517612.1 115886 View on NCBI ↗