Markers + reference

Werauhia

2 species · Bromeliaceae · Poales

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Species 2
Genome length 157–157 kb
Candidate markers 281
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhA SSC 2145 0.0028 1.00 59.1 yes View details
ycf1 SSC 5598 0.0025 1.00 52.0 yes View details
psbA LSC 1062 0.0009 1.00 48.0 yes View details
psbA-trnK-UUU LSC 227 0.0132 1.00 51.8 yes View details
atpH-atpI LSC 948 0.0054 0.98 50.9 yes View details
rpoB-trnC-GCA LSC 1333 0.0045 1.00 53.6 yes View details
accD LSC 1467 0.0048 1.00 61.5 yes View details
accD-psaI LSC 832 0.0048 1.00 56.8 yes View details
petA-psbJ LSC 1136 0.0044 0.99 62.0 yes View details
psbE-petL LSC 1498 0.0040 1.00 61.5 yes View details
rps8 LSC 405 0.0000 1.00 21.1 yes View details
ycf1 IRa 1106 0.0000 1.00 38.5 no View details
rps8-rpl14 LSC 156 0.0321 1.00 70.9 yes View details
ycf1-ndhF SSC 4 0.0000 0.98 70.6 no View details
rps3-rpl22 LSC 46 0.0217 1.00 64.6 yes View details
rps19-psbA LSC 162 0.0186 0.99 63.8 yes View details
rpl36-infA LSC 108 0.0185 1.00 63.1 yes View details
trnF-GAA-ndhJ LSC 766 0.0040 0.98 62.9 yes View details
rbcL-accD LSC 688 0.0030 0.98 62.7 yes View details
matK LSC 1536 0.0052 1.00 61.7 yes View details
atpB-rbcL LSC 771 0.0052 1.00 61.7 yes View details
trnS-GCU-trnG-UCC LSC 1149 0.0018 0.99 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhA_p1 ndhA TGGACCCAATTACCATAGGGA TGGGAGAAGTTGATCGTTGA 2279–2283 1.000 58.9
ndhA_p2 ndhA TGGACCCAATTACCATAGGGA TGGGAGAAGTTGATCGTTGAA 2279–2283 1.000 56.9
ndhA_p3 ndhA TGGACCCAATTACCATAGGGA ATGGGAGAAGTTGATCGTTGA 2280–2284 1.000 55.2
ndhA_p4 ndhA TGGACCCAATTACCATAGGGA CACCCGGTTTTATCAATTTGCA 2375–2379 1.000 54.4
ndhA_p5 ndhA TGGACCCAATTACCATAGGG TGGGAGAAGTTGATCGTTGA 2279–2283 1.000 54.2
ycf1_p1 ycf1 AGACAAATTCTGGGAAGAACCA TCGATATTGAGACCTGGACC 237 1.000 46.5
ycf1_p2 ycf1 TCTGGGAAGAACCAAGATTCT TCGATATTGAGACCTGGACC 229 1.000 44.2
ycf1_p3 ycf1 AGACAAATTCTGGGAAGAACCA ATCGATATTGAGACCTGGACC 238 1.000 42.8
ycf1_p4 ycf1 GACAAATTCTGGGAAGAACCA TCGATATTGAGACCTGGACC 236 1.000 42.6
ycf1_p5 ycf1 TTCTGGGAAGAACCAAGATTCT TCGATATTGAGACCTGGACC 230 1.000 42.1
rps19-psbA_p1 rps19-psbA TCTGACTTTCGCGAGACATG AGCTGTTGTTGAAGCTCCAT 244–245 1.000 78.9
rps19-psbA_p2 rps19-psbA TCTGACTTTCGCGAGACATG ATGCTCACAACTTCCCCCTA 269–270 1.000 78.4
rps19-psbA_p3 rps19-psbA CCTACTCTGACTTTCGCGAG AGCTGTTGTTGAAGCTCCAT 249–250 1.000 77.6
rps19-psbA_p4 rps19-psbA CCTACTCTGACTTTCGCGAG ATGCTCACAACTTCCCCCTA 274–275 1.000 77.1
rps19-psbA_p5 rps19-psbA TCTGACTTTCGCGAGACATG TAATGCTCACAACTTCCCCC 271–272 1.000 77.0
psbA_p1 psbA CAAGATATTGGGTATTGTTCCT GTGCTTGGGAGTCCTTGAAA 1154 1.000 40.1
psbA_p2 psbA CAAGATATTGGGTATTGTTCCT AATACGTGTGCTTGGGAGTC 1161 1.000 40.1
psbA_p3 psbA TGGGTATTGTTCCTTAATTCA GTGCTTGGGAGTCCTTGAAA 1146 1.000 40.1
psbA_p4 psbA CAAGATATTGGGTATTGTTCCTT GTGCTTGGGAGTCCTTGAAA 1154 1.000 40.1
psbA_p5 psbA TGGGTATTGTTCCTTAATTCA AATACGTGTGCTTGGGAGTC 1153 1.000 40.1
psbA-trnK-UUU_p1 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC TGGGGAGGGATCTTTTTCCT 353 1.000 80.0
psbA-trnK-UUU_p2 psbA-trnK-UUU AACACCGAACCATCCAATGT TGGGGAGGGATCTTTTTCCT 419 1.000 77.7
psbA-trnK-UUU_p3 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT TGGGGAGGGATCTTTTTCCT 350 1.000 77.7
psbA-trnK-UUU_p4 psbA-trnK-UUU TCAAAACACCGAACCATCCA TGGGGAGGGATCTTTTTCCT 423 1.000 77.2
psbA-trnK-UUU_p5 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACTCCATCCGACTAGTTCCG 308 1.000 75.8
trnK-UUU_p1 trnK-UUU TTTCAAGGACTCCCAAGCAC TTTGATAGGGTCGTGCAGTG 2962–2966 1.000 79.5
trnK-UUU_p2 trnK-UUU GACTCCCAAGCACACGTATT TTTGATAGGGTCGTGCAGTG 2955–2959 1.000 78.9
trnK-UUU_p3 trnK-UUU TTTCAAGGACTCCCAAGCAC GTCGTGCAGTGCAATTCAAT 2953–2957 1.000 77.6
trnK-UUU_p4 trnK-UUU GACTCCCAAGCACACGTATT GTCGTGCAGTGCAATTCAAT 2946–2950 1.000 77.0
trnK-UUU_p5 trnK-UUU ACACCAATGTCAACCAACCT TTTGATAGGGTCGTGCAGTG 2867–2871 1.000 76.1

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
Werauhia vanhyningii NC_065195.1 157293 View on NCBI ↗
Werauhia werckleana NC_081905.1 157475 View on NCBI ↗