Markers + reference

Puya

10 species · Bromeliaceae · Poales

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Species 10
Genome length 160–160 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 699 0.0065 1.00 54.4 yes View details
trnS-GCU-trnR-UCU LSC 2353 0.0051 1.00 47.9 yes View details
trnT-GGU-psbD LSC 1044 0.0039 1.00 45.9 yes View details
trnS-UGA-psbZ LSC 329 0.0050 1.00 35.2 yes View details
psbZ-trnG-GCC LSC 329 0.0012 1.00 27.9 yes View details
atpB-rbcL LSC 801 0.0043 1.00 55.2 yes View details
ycf1 IRb 1107 0.0009 1.00 45.9 no View details
ndhF-rpl32 SSC 1081 0.0063 1.00 62.3 yes View details
rpl32-trnL-UAG SSC 763 0.0089 1.00 49.3 yes View details
ycf1 SSC 5598 0.0022 1.00 45.9 yes View details
rps3-rpl22 LSC 35 0.0588 0.94 64.5 yes View details
trnG-GCC-trnfM-CAU LSC 140 0.0257 1.00 58.9 yes View details
psbM-trnD-GUC LSC 1045 0.0033 0.99 55.6 yes View details
accD-psaI LSC 944 0.0039 1.00 55.0 yes View details
trnC-GCA-petN LSC 1028 0.0021 1.00 53.3 yes View details
ndhA SSC 2150 0.0031 1.00 52.7 yes View details
rps16-trnQ-UUG LSC 1494 0.0032 1.00 52.5 yes View details
rps15-ycf1 SSC 393 0.0074 1.00 50.9 yes View details
petA-psbJ LSC 1108 0.0035 1.00 50.4 yes View details
ndhH-rps15 SSC 98 0.0154 1.00 50.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCTACGGGAACTG 804–806 1.000 70.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 803–805 1.000 70.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCTACGGGAAC 806–808 1.000 70.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCTACGGGAAC 805–807 1.000 70.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCTACGGGAACT 804–806 1.000 70.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1586–1590 1.000 80.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1584–1588 1.000 80.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1592–1596 1.000 80.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1568–1572 1.000 79.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1579–1583 1.000 78.8
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU GAGAAAGCGGAAAGAGAGGG AGAAGACCTCTGTCCTATCCA 2484–2576 1.000 66.0
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGAAGACCTCTGTCCTATCCA 2429–2521 1.000 65.8
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU GAGAAAGCGGAAAGAGAGGG AGGTTTAGAAGACCTCTGTCCT 2490–2582 1.000 65.3
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGGTTTAGAAGACCTCTGTCCT 2435–2527 1.000 65.2
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AGAAAGCGGAAAGAGAGGGA AGAAGACCTCTGTCCTATCCA 2483–2575 1.000 63.3
trnC-GCA-petN_p1 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGTCCACTCCTTCCCCATAC 1135–1139 1.000 75.9
trnC-GCA-petN_p2 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC GTCCACTCCTTCCCCATACT 1134–1138 1.000 75.9
trnC-GCA-petN_p3 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 1076–1080 1.000 75.6
trnC-GCA-petN_p4 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC GAGTCCACTCCTTCCCCATA 1136–1140 1.000 75.4
trnC-GCA-petN_p5 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC CTAGAGTCCACTCCTTCCCC 1139–1143 1.000 75.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CCTCGCTGGGATTGTAGTTC 1164–1173 1.000 63.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TACACCTCGCTGGGATTGTA 1168–1177 1.000 62.9
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CATACACCTCGCTGGGATTG 1170–1179 1.000 60.7
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA CCTCGCTGGGATTGTAGTTC 1171–1180 1.000 60.4
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1147–1156 1.000 60.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGACCAGCCTACAAAAACGA 1217–1225 1.000 79.4
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1207–1215 1.000 78.3
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1180–1188 1.000 78.0
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CAAAAACGAAACGGTCCCTC 1206–1214 1.000 77.1
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA ACAAAAACGAAACGGTCCCT 1170–1178 1.000 76.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Puya ferruginea NC_062151.1 159713 View on NCBI ↗
Puya goudotiana NC_062150.1 159757 View on NCBI ↗
Puya hamata NC_062154.1 159772 View on NCBI ↗
Puya hutchisonii NC_062152.1 159839 View on NCBI ↗
Puya macropoda NC_062153.1 159828 View on NCBI ↗
Puya macrura NC_062147.1 159826 View on NCBI ↗
Puya mirabilis NC_045380.1 159829 View on NCBI ↗
Puya nitida NC_062146.1 159799 View on NCBI ↗
Puya raimondii NC_062148.1 159785 View on NCBI ↗
Puya santosii NC_062149.1 159752 View on NCBI ↗