Markers + reference

Pereskia

2 species · Cactaceae · Caryophyllales

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Species 2
Genome length 142–142 kb
Candidate markers 242
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 242 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnV-UAC-accD LSC 1397 0.3302 0.84 80.8 yes View details
accD LSC 1530 0.2280 0.91 82.5 yes View details
ndhF SSC 2244 0.2290 0.06 55.4 yes View details
ndhF-rpl32 SSC 1235 0.2759 0.14 75.4 yes View details
ATPE-trnM-CAU LSC 297 0.0657 0.97 82.2 yes View details
rpl33-rps18 LSC 329 0.1003 1.00 74.9 yes View details
trnI-CAU-ycf2 IRb 321 0.0886 0.98 73.1 yes View details
ycf2-trnI-CAU IRa 321 0.0886 0.98 73.1 yes View details
rps19-rpl2 IRb 57 0.0702 1.00 70.6 yes View details
infA-rps8 LSC 112 0.0721 0.99 70.5 yes View details
rps7 SSC 519 0.0424 1.00 70.3 yes View details
trnV-GAC-rrn16 SSC 228 0.0614 1.00 68.1 yes View details
rps3 LSC 657 0.0350 1.00 68.0 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
ATPE-trnM-CAU_p1 ATPE-trnM-CAU AGACACGAGTAGAGGCTACC TATTGCTTTCATACGGCGGG 381 1.000 82.0
ATPE-trnM-CAU_p2 ATPE-trnM-CAU CAGACGAGCTAAGACACGAG TATTGCTTTCATACGGCGGG 392 1.000 80.9
ATPE-trnM-CAU_p3 ATPE-trnM-CAU CTCAGACGAGCTAAGACACG TATTGCTTTCATACGGCGGG 394 1.000 80.9
ATPE-trnM-CAU_p4 ATPE-trnM-CAU AGACGAGCTAAGACACGAGT TATTGCTTTCATACGGCGGG 391 1.000 80.7
ATPE-trnM-CAU_p5 ATPE-trnM-CAU TCAGACGAGCTAAGACACGA TATTGCTTTCATACGGCGGG 393 1.000 80.6
trnV-UAC-accD_p1 trnV-UAC-accD CCGATTCAGGTGCTCGTTTA CCACCGATCCCATACTACCT 2962 0.500 59.9
trnV-UAC-accD_p2 trnV-UAC-accD CCGATTCAGGTGCTCGTTTA CCTACCACCGATCCCATACT 2966 0.500 59.9
trnV-UAC-accD_p3 trnV-UAC-accD CCGATTCAGGTGCTCGTTTA GCGGAATTTTGAGCAAGACC 2687 0.500 59.8
trnV-UAC-accD_p4 trnV-UAC-accD CCGATTCAGGTGCTCGTTTA GGCGGAATTTTGAGCAAGAC 2688 0.500 59.8
trnV-UAC-accD_p5 trnV-UAC-accD CCGATTCAGGTGCTCGTTTA GCGGCATATTCAATCAACCG 2999 0.500 59.7
accD_p1 accD GTTTCGACGGATCCCATTCA CCATTGCAATTGCCGGAAAT 2136–2415 1.000 91.6
accD_p2 accD GAAGACATGGTTTCGACGGA CCATTGCAATTGCCGGAAAT 2145–2424 1.000 91.2
accD_p3 accD GTTTCGACGGATCCCATTCA AAGAAGCCATTGCAATTGCC 2142–2421 1.000 91.0
accD_p4 accD GTTTCGACGGATCCCATTCA GGGGATTCCCGGAAAATCTC 2005 0.500 59.7
accD_p5 accD GAAGACATGGTTTCGACGGA GGGGATTCCCGGAAAATCTC 2014 0.500 59.3
rpl33-rps18_p1 rpl33-rps18 TCTGTCCCTATTGTTACAGACA AAGGGTCGCTTGGATTTATC 402–407 1.000 46.5
rpl33-rps18_p2 rpl33-rps18 TCTGTCCCTATTGTTACAGACA AAAGGGTCGCTTGGATTTATC 403–408 1.000 46.5
rpl33-rps18_p3 rpl33-rps18 TTCTGTCCCTATTGTTACAGACA AAGGGTCGCTTGGATTTATC 403–408 1.000 46.5
rpl33-rps18_p4 rpl33-rps18 TCTGTCCCTATTGTTACAGACAT AAGGGTCGCTTGGATTTATC 402–407 1.000 46.5
rpl33-rps18_p5 rpl33-rps18 TTCTGTCCCTATTGTTACAGACA AAAGGGTCGCTTGGATTTATC 404–409 1.000 46.5
infA-rps8_p1 infA-rps8 ATCTAAACGAACGCGGAACA ATCGGGAAGCTCGACTAGAA 245–246 1.000 84.9
infA-rps8_p2 infA-rps8 TCTAAACGAACGCGGAACAT ATCGGGAAGCTCGACTAGAA 244–245 1.000 84.9
infA-rps8_p3 infA-rps8 TGCGGATCAGACGACATTTT ATCGGGAAGCTCGACTAGAA 599–600 1.000 82.0
infA-rps8_p4 infA-rps8 GTGCACTCTTACGCGAACTA ATCGGGAAGCTCGACTAGAA 852–854 1.000 81.7
infA-rps8_p5 infA-rps8 GTGCACTCTTACGCGAACTA AAAAAGAGTCAGTCGGCCTG 965–967 1.000 81.0
rps3_p1 rps3 AGACAAGTCAAGTAAAGGCT ACAAGTTTGGGCTGCAGTAA 774 1.000 51.4
rps3_p2 rps3 AGACAAGTCAAGTAAAGGCT GGGCTGCAGTAAACTCTTCA 766 1.000 50.5
rps3_p3 rps3 AGACAAGTCAAGTAAAGGCT TGGGCTGCAGTAAACTCTTC 767 1.000 50.5
rps3_p4 rps3 AGACAAGTCAAGTAAAGGCTT ACAAGTTTGGGCTGCAGTAA 774 1.000 50.4
rps3_p5 rps3 AAGACAAGTCAAGTAAAGGCT ACAAGTTTGGGCTGCAGTAA 775 1.000 50.3

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
Pereskia aculeata NC_062888.1 141998 View on NCBI ↗
Pereskia humboldtii OR711232.1 142275 View on NCBI ↗