Markers + reference

Consolea

2 species · Cactaceae · Caryophyllales

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Species 2
Genome length 161–161 kb
Candidate markers 284
Primer pairs 85

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 8 remaining regions by MarkerSeek score (out of 284 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps8 LSC 405 0.0049 1.00 57.5 yes View details
rpoC2 LSC 4065 0.0005 1.00 54.2 yes View details
psbZ-trnG-GCC LSC 367 0.0027 1.00 55.5 yes View details
ndhK LSC 678 0.0000 1.00 26.9 yes View details
accD LSC 3171 0.0016 1.00 56.3 yes View details
ndhG-trnL-UAG IRb 252 0.0040 1.00 47.1 yes View details
ndhK-ndhC LSC 58 0.0172 1.00 62.4 yes View details
rpoB-trnC-GCA LSC 1141 0.0000 0.99 59.3 yes View details
psbE-rps12 LSC 1168 0.0009 1.00 59.2 yes View details
ndhF-rpl32 IRb 1259 0.0008 1.00 59.2 yes View details
rpl32-ndhF IRa 1259 0.0008 1.00 59.2 yes View details
atpF LSC 1308 0.0000 1.00 59.0 yes View details
trnT-GGU-psbD LSC 1297 0.0000 1.00 58.8 yes View details
trnI-CAU-ycf2 IRb 135 0.0074 1.00 56.8 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
rps8_p1 rps8 AAATTCGGAGACACCACTGA GGGACCAACTAATAGGGGGA 526 1.000 68.9
rps8_p2 rps8 TCGGAGACACCACTGATTTT GGGACCAACTAATAGGGGGA 522 1.000 68.9
rps8_p3 rps8 TTCGGAGACACCACTGATTT GGGACCAACTAATAGGGGGA 523 1.000 68.9
rps8_p4 rps8 TCGGAGACACCACTGATTTT AGGGACCAACTAATAGGGGG 523 1.000 68.9
rps8_p5 rps8 TTCGGAGACACCACTGATTT AGGGACCAACTAATAGGGGG 524 1.000 68.9
trnG-UCC_p1 trnG-UCC TCGACAAAAGGTTCAGCTCA TGGATTGTACGCGAGATGAG 880–881 1.000 71.3
trnG-UCC_p2 trnG-UCC AGCTCGACAAAAGGTTCAGC TGGATTGTACGCGAGATGAG 883–884 1.000 70.0
trnG-UCC_p3 trnG-UCC GCTCGACAAAAGGTTCAGCT TGGATTGTACGCGAGATGAG 882–883 1.000 70.0
trnG-UCC_p4 trnG-UCC TCGACAAAAGGTTCAGCTCA GGATTGTACGCGAGATGAGA 879–880 1.000 69.0
trnG-UCC_p5 trnG-UCC GCTCGACAAAAGGTTCAGCT GGATTGTACGCGAGATGAGA 881–882 1.000 67.7
atpF_p1 atpF AGGGTTGCCATGAGTCTTTC GTAGCAAAGAGGTGAGGCAA 1441–1445 1.000 77.1
atpF_p2 atpF GAAGGGTTGCCATGAGTCTT GTAGCAAAGAGGTGAGGCAA 1443–1447 1.000 77.1
atpF_p3 atpF GGGTTGCCATGAGTCTTTCT GTAGCAAAGAGGTGAGGCAA 1440–1444 1.000 77.1
atpF_p4 atpF AGGGTTGCCATGAGTCTTTC GAGGTGAGGCAATACAACGA 1433–1437 1.000 75.5
atpF_p5 atpF GGGTTGCCATGAGTCTTTCT GAGGTGAGGCAATACAACGA 1432–1436 1.000 75.5
rpoC2_p1 rpoC2 CGCCTCTTTGCCAATAAATCA ACTGATGTGTACCATGCACC 335 1.000 65.1
rpoC2_p2 rpoC2 CGCCTCTTTGCCAATAAATCA ATCAGGAAGGCCGTACAGAT 258 1.000 64.4
rpoC2_p3 rpoC2 CGCCTCTTTGCCAATAAATCA ACCATGCACCCGAATTTACA 325 1.000 64.3
rpoC2_p4 rpoC2 CGCCTCTTTGCCAATAAATCA TGTACCATGCACCCGAATTT 328 1.000 64.3
rpoC2_p5 rpoC2 CGCCTCTTTGCCAATAAATCA GGGGAAATGCACTGGAGTAC 353 1.000 64.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATTTTCATCCCGTAGCA ATTAGAATCAGGCGACACCC 1237–1243 1.000 66.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTCATTTTCATCCCGTAGCA CGACACCCAGATTCGAACTG 1225–1231 1.000 66.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTCATTTTCATCCCGTAGCA TTAGAATCAGGCGACACCCA 1236–1242 1.000 65.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTTCATCCCGT ATTAGAATCAGGCGACACCC 1240–1246 1.000 65.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCCCTCATTTTCATCCCGT CGACACCCAGATTCGAACTG 1228–1234 1.000 65.6
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TCCCTCCGTAACCAGTCATC 1431–1432 1.000 75.4
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TCCCTCCGTAACCAGTCATC 1434–1435 1.000 75.2
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TCCCTCCGTAACCAGTCATC 1408–1409 1.000 73.6
trnT-GGU-psbD_p4 trnT-GGU-psbD GGCCCTTTTAACTCAGTGGT TCCCTCCGTAACCAGTCATC 1446–1447 1.000 73.6
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GCAATAGACCAGACCAACCT 1466–1467 1.000 73.2

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
Consolea macracantha NC_083925.1 160649 View on NCBI ↗
Consolea rubescens NC_083927.1 160830 View on NCBI ↗