Markers + reference

Viridantha

3 species · Bromeliaceae · Poales

Back to catalogue

Species 3
Genome length 157–157 kb
Candidate markers 280
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaC-ndhE SSC 400 0.0152 0.99 61.2 yes View details
ndhE SSC 306 0.0044 1.00 47.2 yes View details
ycf1 SSC 5601 0.0058 1.00 41.4 yes View details
trnS-GCU-trnG-UCC LSC 1062 0.0116 0.98 62.8 yes View details
trnT-UGU-trnL-UAA LSC 478 0.0063 1.00 60.5 yes View details
trnM-CAU-atpE LSC 171 0.0468 1.00 69.8 yes View details
petA-psbJ LSC 1139 0.0070 1.00 64.9 yes View details
psbE-petL LSC 1494 0.0036 1.00 61.5 yes View details
ycf1 IRa 1110 0.0042 1.00 61.4 yes View details
matK-trnK-UUU LSC 812 0.0082 1.00 64.8 yes View details
rps8-rpl14 LSC 167 0.0160 1.00 62.7 yes View details
ndhC-trnV-UAC LSC 1050 0.0038 0.99 62.0 yes View details
psbM-trnD-GUC LSC 1027 0.0046 1.00 61.9 yes View details
atpH-atpI LSC 994 0.0040 1.00 61.3 yes View details
rpl32-trnL-UAG SSC 762 0.0035 1.00 61.1 yes View details
ccsA SSC 954 0.0035 1.00 61.0 yes View details
rpoB-trnC-GCA LSC 1387 0.0024 1.00 60.9 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 849–852 1.000 76.2
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT CAGCGTGTCTACCGATTTCA 850–853 1.000 76.2
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT TTTAGAAGATGCCGCCACTC 909–912 1.000 76.0
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TTCCACCGGGCATTCAAAAA AGCGTGTCTACCGATTTCAC 852–855 1.000 75.7
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TTTCCACCGGGCATTCAAAA AGCGTGTCTACCGATTTCAC 853–856 1.000 75.7
ccsA_p1 ccsA GAGTGGCGGCATCTTCTAAA TGGTTCTCAAAAACTCATAAAAACA 1134 1.000 40.4
ccsA_p2 ccsA GAGTGGCGGCATCTTCTAAA ACTTTCGTTATATATGGGATGATGT 1108 1.000 40.4
ccsA_p3 ccsA GCTAAAGCATCTCGGTTCGA ACTTTCGTTATATATGGGATGATGT 1132 1.000 40.4
ccsA_p4 ccsA GAGTGGCGGCATCTTCTAAA ACTCATAAAAACAAACTTTCGT 1122 1.000 40.4
ccsA_p5 ccsA GCTAAAGCATCTCGGTTCGA TGGTTCTCAAAAACTCATAAAAACA 1158 1.000 40.3
psaC-ndhE_p1 psaC-ndhE TTGCTTGGCTTTACATCCGT TTATAGCCATTGCAGCTGCT 619–624 1.000 78.2
psaC-ndhE_p2 psaC-ndhE ACATCCGTCCCAAGGTATCA TTATAGCCATTGCAGCTGCT 607–612 1.000 78.0
psaC-ndhE_p3 psaC-ndhE TTGCTTGGCTTTACATCCGT TATAGCCATTGCAGCTGCTG 618–623 1.000 77.9
psaC-ndhE_p4 psaC-ndhE CCAATACATCTGTGGGGCAA TTATAGCCATTGCAGCTGCT 584–589 1.000 77.9
psaC-ndhE_p5 psaC-ndhE TTGCTTGGCTTTACATCCGT GTTATAGCCATTGCAGCTGC 620–625 1.000 77.7
ndhE_p1 ndhE CATGCTGCGAGTTGTTTCAG GACTGCAAGGTCAAACCAGA 1289–1294 1.000 80.5
ndhE_p2 ndhE TTGCTTGGCTTTACATCCGT GACTGCAAGGTCAAACCAGA 1172–1177 1.000 80.1
ndhE_p3 ndhE ACATCCGTCCCAAGGTATCA GACTGCAAGGTCAAACCAGA 1160–1165 1.000 79.9
ndhE_p4 ndhE CCAATACATCTGTGGGGCAA GACTGCAAGGTCAAACCAGA 1137–1142 1.000 79.8
ndhE_p5 ndhE CGAGTTGTTTCAGGCCCTAA GACTGCAAGGTCAAACCAGA 1282–1287 1.000 79.4
ycf1_p1 ycf1 ATCAAAGCCACCTCTTCTGC GTTCCTCGGTGGTCATACAA 203 1.000 75.4
ycf1_p2 ycf1 ACGAAAATCCGATTGTTGCG GTTCCTCGGTGGTCATACAA 231 1.000 74.5
ycf1_p3 ycf1 TTACGTCTTTGAGCACGCAT GTTCCTCGGTGGTCATACAA 272 1.000 74.3
ycf1_p4 ycf1 TCCCGACGAAAATCCGATTG GTTCCTCGGTGGTCATACAA 236 1.000 73.5
ycf1_p5 ycf1 CGTCTTTGAGCACGCATAGA GTTCCTCGGTGGTCATACAA 269 1.000 73.1
trnK-UUU_p1 trnK-UUU TTTCAAGGACTCCCAAGCAC TTTGATAGGGTCGTGCAGTG 2961–2971 1.000 80.2
trnK-UUU_p2 trnK-UUU GACTCCCAAGCACACGTATT TTTGATAGGGTCGTGCAGTG 2954–2964 1.000 79.6
trnK-UUU_p3 trnK-UUU TTTCAAGGACTCCCAAGCAC GTCGTGCAGTGCAATTCAAT 2952–2962 1.000 78.2
trnK-UUU_p4 trnK-UUU GACTCCCAAGCACACGTATT GTCGTGCAGTGCAATTCAAT 2945–2955 1.000 77.6
trnK-UUU_p5 trnK-UUU TTTCAAGGACTCCCAAGCAC TGTTTTGATAGGGTCGTGCA 2964–2974 1.000 76.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Viridantha ignesiae NC_065183.1 156918 View on NCBI ↗
Viridantha plumosa NC_081704.1 157179 View on NCBI ↗
Viridantha tortilis NC_081742.1 157063 View on NCBI ↗