Markers + reference

Opuntia

6 species · Cactaceae · Caryophyllales

Back to catalogue

Species 6
Genome length 138–150 kb
Candidate markers 268
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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf2 Genome 6574 0.0095 0.05 33.6 yes View details
accD Genome 3720 0.0363 0.94 74.2 yes View details
ycf1 Genome 2853 0.0097 1.00 54.0 no View details
ycf1 Genome 2853 0.0097 1.00 53.9 yes View details
trnF-GAA-ndhJ Genome 786 0.0165 1.00 63.9 yes View details
ndhF-rpl32 Genome 1421 0.0024 0.97 60.8 yes View details
rpl32-ndhF Genome 1421 0.0025 0.97 60.8 yes View details
petD Genome 1270 0.0016 1.00 60.4 yes View details
rpl32-ycf1 Genome 58 0.0316 0.98 56.6 yes View details
ycf1-rpl32 Genome 58 0.0304 0.98 56.1 yes View details
psbA-trnH-GUG Genome 372 0.0065 0.99 55.3 yes View details
psaA-ycf3 Genome 821 0.0032 0.97 54.9 yes View details
psaJ-trnP-UGG Genome 415 0.0061 1.00 54.8 yes View details
ndhC-rbcL Genome 798 0.0036 0.98 54.4 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf2_p1 ycf2 AATCATGGTCCTTGCGGATC CTTTGACCCCCGAATTTGGA 512 0.500 59.9
ycf2_p2 ycf2 AATCATGGTCCTTGCGGATC TCTTTGACCCCCGAATTTGG 513 0.500 59.9
ycf2_p3 ycf2 AATCATGGTCCTTGCGGATC TTTGACCCCCGAATTTGGAG 511 0.500 59.9
ycf2_p4 ycf2 GTACGGATTCTTCCCCCAAC CTTTGACCCCCGAATTTGGA 817 0.500 59.8
ycf2_p5 ycf2 GTACGGATTCTTCCCCCAAC TTTGACCCCCGAATTTGGAG 816 0.500 59.8
petD_p1 petD ACTTTTGAAGCGACTATTCCCT TGGACATTTTCCTTCAACTCCA 1422–1428 1.000 45.0
petD_p2 petD CACTTTTGAAGCGACTATTCCC TGGACATTTTCCTTCAACTCCA 1423–1429 1.000 44.5
petD_p3 petD ACTTTTGAAGCGACTATTCCCT GGACATTTTCCTTCAACTCCAC 1421–1427 1.000 42.3
petD_p4 petD CACTTTTGAAGCGACTATTCCC GGACATTTTCCTTCAACTCCAC 1422–1428 1.000 41.9
petD_p5 petD TCCGAATAGGCCCATAATTTCA TGGACATTTTCCTTCAACTCCA 1476–1482 1.000 41.5
psaA-ycf3_p1 psaA-ycf3 GTCTGGCCCATTCCTCAAAA CGATAACGCTTACTCCCGAG 950–982 1.000 81.9
psaA-ycf3_p2 psaA-ycf3 GTTCTTGAAAAATGGCCCGG CGATAACGCTTACTCCCGAG 969–1001 1.000 81.8
psaA-ycf3_p3 psaA-ycf3 GTCTGGCCCATTCCTCAAAA ATCAAGCCGCTGAGTATTGG 977–1009 1.000 81.7
psaA-ycf3_p4 psaA-ycf3 GTTCTTGAAAAATGGCCCGG ATCAAGCCGCTGAGTATTGG 996–1028 1.000 81.7
psaA-ycf3_p5 psaA-ycf3 GTCTGGCCCATTCCTCAAAA CGATCAAGCCGCTGAGTATT 979–1011 1.000 80.9
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA AGTTGGATAGGATGGCCCTT 928–978 1.000 82.6
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA AGTTGGATAGGATGGCCCTT 892–942 1.000 82.3
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA TAATCACCCACGCCTGAAAC 965–1015 1.000 81.7
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CTGGTAGAGCAGAGGACTGA AGTTGGATAGGATGGCCCTT 916–966 1.000 81.6
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TAATCACCCACGCCTGAAAC 929–979 1.000 81.4
ndhC-rbcL_p1 ndhC-rbcL GTCCTTTGCTAATCGGAGCT AAATTTGAGTTCCCGGCAGT 939–961 1.000 79.6
ndhC-rbcL_p2 ndhC-rbcL GTCCTTTGCTAATCGGAGCT GCTGCTTGTGAGGTATGGAA 966–988 1.000 78.7
ndhC-rbcL_p3 ndhC-rbcL GTCCTTTGCTAATCGGAGCT CGGCAGTGGATACTTTGGAT 926–948 1.000 77.0
ndhC-rbcL_p4 ndhC-rbcL CTGGTCCTTTGCTAATCGGA AAATTTGAGTTCCCGGCAGT 942–964 1.000 76.6
ndhC-rbcL_p5 ndhC-rbcL TGGTCCTTTGCTAATCGGAG AAATTTGAGTTCCCGGCAGT 941–963 1.000 76.6
accD_p1 accD CTCTGGGTCCGGATAAGGAT GCTCCCATAGAACCCCCTAT 880–1180 0.833 83.1
accD_p2 accD CTCTGGGTCCGGATAAGGAT CTAGTGGGCGATGCAAGAAT 1093–1393 0.833 82.2
accD_p3 accD CTCTGGGTCCGGATAAGGAT TTTTCGGTTGTTTGTGCACC 1234–1534 0.833 82.0
accD_p4 accD GGATGAGGATTGTCGAACCC TTTTCGGTTGTTTGTGCACC 1377 0.167 46.3
accD_p5 accD GGGATGAGGATTGTCGAACC TTTTCGGTTGTTTGTGCACC 1378 0.167 46.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Opuntia arechavaletae NC_083929.1 149275 View on NCBI ↗
Opuntia auberi NC_083930.1 138379 View on NCBI ↗
Opuntia caracassana NC_083933.1 138141 View on NCBI ↗
Opuntia gaumeri NC_083939.1 137818 View on NCBI ↗
Opuntia quimilo NC_083949.1 150374 View on NCBI ↗
Opuntia retrorsa NC_083951.1 147640 View on NCBI ↗