Markers + reference

Hylotelephium

8 species · Crassulaceae · Saxifragales

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Species 8
Genome length 150–152 kb
Candidate markers 267
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0017 1.00 34.9 yes View details
rps16-trnQ-UUG LSC 1275 0.0193 0.99 60.8 yes View details
accD-psaI LSC 555 0.0109 0.99 40.0 yes View details
ycf1 IRb 1079 0.0021 1.00 41.0 no View details
rpl32-trnL-UAG SSC 439 0.0360 0.89 65.3 yes View details
ndhA SSC 2185 0.0066 0.99 44.1 yes View details
ycf1 SSC 5163 0.0088 1.00 47.9 yes View details
trnH-GUG-psbA LSC 239 0.0306 1.00 68.3 yes View details
psbE-petL LSC 1174 0.0087 0.99 57.3 yes View details
ndhF-rpl32 SSC 585 0.0123 0.98 56.9 yes View details
trnL-UAG-ccsA SSC 71 0.0302 1.00 56.6 yes View details
psbK-psbI LSC 404 0.0081 0.99 55.3 yes View details
rps15-ycf1 SSC 403 0.0107 1.00 52.9 yes View details
trnE-UUC-trnT-GGU LSC 826 0.0053 0.99 51.7 yes View details
rpl20-rps12 LSC 793 0.0013 1.00 51.2 yes View details
trnG-GCC-trnR-UCU LSC 231 0.0145 1.00 50.8 yes View details
psbL-psbF LSC 22 0.0244 1.00 50.4 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 299–328 1.000 85.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 302–331 1.000 85.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 313–342 1.000 85.4
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 312–341 1.000 85.4
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 314–343 1.000 85.3
psbA_p1 psbA ACTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1136 1.000 40.4
psbA_p2 psbA AACTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1137 1.000 40.4
psbA_p3 psbA ACTCGTATAGACTAATACCGAAGTT ATTTGGTTGCTTGGGAGTCC 1136 1.000 40.4
psbA_p4 psbA ACTCGTATAGACTAATACCGAAG ATTTGGTTGCTTGGGAGTCC 1136 1.000 40.4
psbA_p5 psbA CTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1135 1.000 40.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 441–1363 1.000 85.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 452–1374 1.000 85.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTATGCGGAGGTTCGAATCC 448–1370 1.000 84.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTATGCGGAGGTTCGAATCC 459–1381 1.000 84.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ATTTAAATGCAGTGGGGCGT 501–1424 1.000 82.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CTTCTCGTCCAGGATTACGTC 534–540 1.000 73.4
psbK-psbI_p2 psbK-psbI TGCCAGTTATACCCCTGCTA CTTCTCGTCCAGGATTACGTC 572–578 1.000 72.2
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTCGTCCAGGATTACGTC 533–539 1.000 72.2
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG CTTCTCGTCCAGGATTACGT 534–540 1.000 72.1
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCTCGTCCAGGATTACGT 535–541 1.000 71.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGGTTTAGAAGACCTATGTCCT 317–320 1.000 48.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA AGGTTTAGAAGACCTATGTCCT 344–347 1.000 48.5
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGAAGACCTATGTCCTATCCA 311–314 1.000 48.4
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA AGAAGACCTATGTCCTATCCA 338–341 1.000 48.3
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA ACCAAAGGTTTAGAAGACCTATGT 349–352 1.000 47.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG GAACCGATGACTTACGCCTT 946–966 1.000 83.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG CCATGGCGTTACTCTACCAC 925–945 1.000 82.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG TGGCGTTACTCTACCACTGA 922–942 1.000 82.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG CCGATGACTTACGCCTTACC 943–963 1.000 82.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 911–931 1.000 81.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Hylotelephium erythrostictum NC_072126.1 151675 View on NCBI ↗
Hylotelephium ewersii MN794014.1 151699 View on NCBI ↗
Hylotelephium pallescens NC_072127.1 151717 View on NCBI ↗
Hylotelephium spectabile NC_072128.1 151793 View on NCBI ↗
Hylotelephium ussuriense NC_072129.1 151329 View on NCBI ↗
Hylotelephium verticillatum NC_052738.1 151398 View on NCBI ↗
Hylotelephium viridescens NC_072130.1 151650 View on NCBI ↗
Hylotelephium viviparum NC_063661.1 150429 View on NCBI ↗