Markers + reference

Vriesea

4 species · Bromeliaceae · Poales

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Species 4
Genome length 157–158 kb
Candidate markers 281
Primer pairs 85

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 10 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 753 0.0060 1.00 49.6 yes View details
ycf1 SSC 5451 0.0034 1.00 40.0 yes View details
psbK-psbI LSC 420 0.0083 1.00 48.8 yes View details
trnG-GCC-psbZ LSC 317 0.0063 1.00 52.7 yes View details
psbC LSC 1422 0.0012 1.00 39.1 yes View details
petA-psbJ LSC 1133 0.0087 1.00 62.1 yes View details
trnP-UGG-psaJ LSC 337 0.0015 1.00 37.6 yes View details
ycf1 IRa 991 0.0007 1.00 35.1 no View details
ndhF-rpl32 SSC 973 0.0082 0.97 80.4 no View details
ycf3-psaA LSC 633 0.0039 1.00 62.6 yes View details
rbcL-atpB LSC 777 0.0047 1.00 62.2 yes View details
trnV-UAC-ndhC LSC 802 0.0027 1.00 61.3 yes View details
psbD-psaI LSC 1672 0.0032 1.00 61.2 yes View details
trnL-UAA-trnT-UGU LSC 771 0.0035 1.00 60.9 yes View details
psbM-trnD-GUC LSC 1031 0.0024 1.00 60.4 yes View details
accD-rbcL LSC 692 0.0014 1.00 60.3 yes View details
matK-trnK-UUU LSC 823 0.0018 1.00 60.2 yes View details
atpF LSC 1396 0.0014 1.00 59.7 yes View details
rpl16-rps3 LSC 145 0.0080 1.00 59.5 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 85 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 837–840 1.000 77.0
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT CAGCGTGTCTACCGATTTCA 838–841 1.000 77.0
rpl32-trnL-UAG_p3 rpl32-trnL-UAG TTCCACCGGGCATTCAAAAA AGCGTGTCTACCGATTTCAC 840–843 1.000 76.5
rpl32-trnL-UAG_p4 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT ATCCGCATAAAAGAGCTGCA 1423–1426 1.000 76.2
rpl32-trnL-UAG_p5 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT TCCGCATAAAAGAGCTGCAT 1422–1425 1.000 76.2
ycf1_p1 ycf1 TCTTGTCTTTTGTGATTCGTTCT AGGAAATTCAAAAAGTAAACCCA 237 1.000 41.4
ycf1_p2 ycf1 TCTTGTCTTTTGTGATTCGTTCT AGGAAATTCAAAAAGTAAACCCAA 237 1.000 41.4
ycf1_p3 ycf1 TCTTGTCTTTTGTGATTCGTTCT TGAAGGAAATTCAAAAAGTAAACCCA 240 1.000 41.3
ycf1_p4 ycf1 TCTTGTCTTTTGTGATTCGTTCT GAAGGAAATTCAAAAAGTAAACCCA 239 1.000 41.3
ycf1_p5 ycf1 TCTTGTCTTTTGTGATTCGTTCT TGAAGGAAATTCAAAAAGTAAACCC 240 1.000 41.3
matK-trnK-UUU_p1 matK-trnK-UUU CCATGATCATGAGCAAACGC TTTGATAGGGTCGTGCAGTG 1037–1040 1.000 78.6
matK-trnK-UUU_p2 matK-trnK-UUU CCATGATCATGAGCAAACGC ATCCGGGTTGCTAACTCAAC 970–973 1.000 78.5
matK-trnK-UUU_p3 matK-trnK-UUU TAGGAAGTGTTGTTGCCGAG TTTGATAGGGTCGTGCAGTG 987–990 1.000 78.3
matK-trnK-UUU_p4 matK-trnK-UUU TAGGAAGTGTTGTTGCCGAG ATCCGGGTTGCTAACTCAAC 920–923 1.000 78.2
matK-trnK-UUU_p5 matK-trnK-UUU CCATGATCATGAGCAAACGC ACGGTAGAGTACTCGGCTTT 952–955 1.000 78.1
psbK-psbI_p1 psbK-psbI CAAGCCGCTGTAAGTTTTCG GGATTGCGTCCTGGATCATT 539–542 1.000 80.3
psbK-psbI_p2 psbK-psbI AGCCGCTGTAAGTTTTCGAT GGATTGCGTCCTGGATCATT 537–540 1.000 79.9
psbK-psbI_p3 psbK-psbI AAGCCGCTGTAAGTTTTCGA GGATTGCGTCCTGGATCATT 538–541 1.000 79.7
psbK-psbI_p4 psbK-psbI GCCGCTGTAAGTTTTCGATG GGATTGCGTCCTGGATCATT 536–539 1.000 79.4
psbK-psbI_p5 psbK-psbI GCAAGCCGCTGTAAGTTTTC GGATTGCGTCCTGGATCATT 540–543 1.000 78.2
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA GGGCGAGCGAAGTAATAGAA 1569–1591 1.000 71.0
atpF_p2 atpF GGCTCGAAGGGTTACCATTA GGGCGAGCGAAGTAATAGAA 1557–1579 1.000 68.2
atpF_p3 atpF ACTAATTTCGTCGGCTCGAA AAGGGGCGAGCGAAGTAATA 1572–1594 1.000 68.0
atpF_p4 atpF GGCTCGAAGGGTTACCATTAG GGGCGAGCGAAGTAATAGAA 1557–1579 1.000 66.9
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA GGGCGAGCGAAGTAATAGAAA 1569–1591 1.000 65.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CCTCGCTGGGATTGTAGTTC 1159–1161 1.000 62.0
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TACACCTCGCTGGGATTGTA 1163–1165 1.000 61.4
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CATACACCTCGCTGGGATTG 1165–1167 1.000 59.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA CCTCGCTGGGATTGTAGTTC 1166–1168 1.000 58.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1142–1144 1.000 58.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Vriesea friburgensis NC_081752.1 157587 View on NCBI ↗
Vriesea saundersii NC_065192.1 157850 View on NCBI ↗
Vriesea sucrei NC_065193.1 157278 View on NCBI ↗
Vriesea vagans NC_081753.1 157756 View on NCBI ↗