Markers + reference

Wallisia

2 species · Bromeliaceae · Poales

Back to catalogue

Species 2
Genome length 157–157 kb
Candidate markers 281
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl32-trnL-UAG SSC 760 0.0013 1.00 59.5 yes View details
ndhI SSC 543 0.0018 1.00 58.6 yes View details
ndhA SSC 2145 0.0005 1.00 57.7 yes View details
rps15 SSC 273 0.0000 1.00 30.8 yes View details
rps15-ycf1 SSC 403 0.0074 1.00 58.9 yes View details
rps19 IRb 279 0.0000 1.00 23.7 yes View details
psbA LSC 1062 0.0000 1.00 30.8 yes View details
trnS-GCU-trnG-UCC LSC 1185 0.0017 1.00 49.6 yes View details
atpF LSC 1387 0.0029 1.00 60.4 yes View details
petA-psbJ LSC 1121 0.0018 1.00 59.8 yes View details
rps19 IRa 279 0.0000 1.00 33.8 no View details
ycf1-ndhF SSC 3 0.0000 0.98 70.7 no View details
rps19-psbA LSC 145 0.0138 1.00 60.4 yes View details
accD-psaI LSC 606 0.0016 1.00 59.7 yes View details
atpH-atpI LSC 998 0.0000 0.99 59.2 yes View details
rpoB-trnC-GCA LSC 1341 0.0007 1.00 59.2 yes View details
accD LSC 1461 0.0007 1.00 59.1 yes View details
rpl20-rps12 LSC 704 0.0000 1.00 58.9 yes View details
clpP LSC 2113 0.0005 1.00 57.7 yes View details
psbA-trnK-UUU LSC 230 0.0087 1.00 57.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl32-trnL-UAG_p1 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT AGCGTGTCTACCGATTTCAC 847 1.000 75.8
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT CAGCGTGTCTACCGATTTCA 848 1.000 75.8
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT TTTAGAAGATGCCGCCACTC 907 1.000 75.7
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TTCCACCGGGCATTCAAAAA AGCGTGTCTACCGATTTCAC 850 1.000 75.3
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TTTCCACCGGGCATTCAAAA AGCGTGTCTACCGATTTCAC 851 1.000 75.3
ndhI_p1 ndhI CCCAAAATAAAAAGCTTGGATCCT ACAACTTCTTCCCAACTTGT 703 1.000 40.1
ndhI_p2 ndhI ACCCAAAATAAAAAGCTTGGATCC ACAACTTCTTCCCAACTTGT 704 1.000 40.1
ndhI_p3 ndhI CCCAAAATAAAAAGCTTGGATCCT AACAACTTCTTCCCAACTTGT 704 1.000 40.1
ndhI_p4 ndhI CCCAAAATAAAAAGCTTGGATCCT ACAACTTCTTCCCAACTTGTT 703 1.000 40.1
ndhI_p5 ndhI ACCCAAAATAAAAAGCTTGGATCC ACAACTTCTTCCCAACTTGTT 704 1.000 40.1
ndhA_p1 ndhA TGGACCCAATTACCATAGGGA TGGGAGAAGTTGATCGTTGA 2279 1.000 58.7
ndhA_p2 ndhA TGGACCCAATTACCATAGGGA TGGGAGAAGTTGATCGTTGAA 2279 1.000 56.7
ndhA_p3 ndhA TGGACCCAATTACCATAGGGA ATGGGAGAAGTTGATCGTTGA 2280 1.000 55.0
ndhA_p4 ndhA TGGACCCAATTACCATAGGGA CACCCGGTTTTATCAATTTGCA 2375 1.000 54.2
ndhA_p5 ndhA TGGACCCAATTACCATAGGG TGGGAGAAGTTGATCGTTGA 2279 1.000 54.0
rps15_p1 rps15 TCTTGTAACCGGTACTGTCA TCCTGATCGGAAAAATCCATGA 446 1.000 42.7
rps15_p2 rps15 TCCTCAAAACGAGACTCATCA TCCTGATCGGAAAAATCCATGA 392 1.000 41.5
rps15_p3 rps15 TTCTTGTAACCGGTACTGTCA TCCTGATCGGAAAAATCCATGA 447 1.000 41.0
rps15_p4 rps15 TCTTGTAACCGGTACTGTCAT TCCTGATCGGAAAAATCCATGA 446 1.000 40.0
rps15_p5 rps15 TCCTCAAAACGAGACTCATCAA TCCTGATCGGAAAAATCCATGA 392 1.000 40.0
rps15-ycf1_p1 rps15-ycf1 CAAATGTGAAGTAAGTCTCCGT TGGCAGTCGTTTCAGTATGT 581–582 1.000 44.9
rps15-ycf1_p2 rps15-ycf1 AGTCTCCGTATCTTATTGGTGA TGGCAGTCGTTTCAGTATGT 568–569 1.000 42.6
rps15-ycf1_p3 rps15-ycf1 TGTGAAGTAAGTCTCCGTATCT TGGCAGTCGTTTCAGTATGT 577–578 1.000 42.2
rps15-ycf1_p4 rps15-ycf1 AATGTGAAGTAAGTCTCCGT TGGCAGTCGTTTCAGTATGT 579–580 1.000 42.0
rps15-ycf1_p5 rps15-ycf1 CAAATGTGAAGTAAGTCTCCGT GGCAGTCGTTTCAGTATGTCA 580–581 1.000 41.1
rps19_p1 rps19 TCTGACCTCCATACTTAGATCGA TCTATTCTTAATTCCAAATTCCAA 388 1.000 40.0
rps19_p2 rps19 TCTGACCTCCATACTTAGATCGA TTCTATTCTTAATTCCAAATTCCA 389 1.000 40.0
rps19_p3 rps19 TGACCTCCATACTTAGATCGAGA TCTATTCTTAATTCCAAATTCCAA 386 1.000 40.0
rps19_p4 rps19 TGACCTCCATACTTAGATCGAGA TTCTATTCTTAATTCCAAATTCCA 387 1.000 40.0
rps19_p5 rps19 CTGACCTCCATACTTAGATCGAG TCTATTCTTAATTCCAAATTCCAA 387 1.000 40.0

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
Wallisia cyanea NC_065194.1 157200 View on NCBI ↗
Wallisia lindeniana NC_081754.1 157224 View on NCBI ↗