Markers + reference

Stylidium

2 species · Stylidiaceae · Asterales

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Species 2
Genome length 150–151 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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 801 0.0517 0.97 77.5 yes View details
trnC-GCA-petN LSC 788 0.0374 0.95 74.5 yes View details
accD-psaI LSC 747 0.0376 0.96 69.0 yes View details
petA-psbJ LSC 1014 0.0715 0.98 82.4 yes View details
ycf1 SSC 5283 0.0259 1.00 53.7 yes View details
trnL-UAG-rpl32 SSC 564 0.0525 0.98 75.3 yes View details
rpl32-ndhF SSC 968 0.0407 0.91 72.3 yes View details
trnS-GGA-rps4 LSC 180 0.0944 1.00 80.4 yes View details
atpF-atpH LSC 287 0.0507 0.96 79.2 yes View details
ndhA-ndhI SSC 86 0.0476 0.98 78.8 yes View details
rps16-trnQ-UUG LSC 353 0.0562 0.96 75.4 yes View details
petL-petG LSC 182 0.0686 0.96 73.7 yes View details
ndhC-trnV-UAC LSC 1154 0.0283 0.98 73.5 yes View details
infA-rps8 LSC 93 0.0753 1.00 72.9 yes View details
matK-trnK-UUU LSC 733 0.0447 0.98 72.5 yes View details
rps8-rpl14 LSC 183 0.0710 1.00 71.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU AGTAGCGAAGAACTTGCACC AACGGTAGAGTACTCGGCTT 1244 0.500 57.0
matK-trnK-UUU_p2 matK-trnK-UUU AGTAGCGAAGAACTTGCACC ACGGTAGAGTACTCGGCTTT 1243 0.500 57.0
matK-trnK-UUU_p3 matK-trnK-UUU TAGCGAAGAACTTGCACCAA AACGGTAGAGTACTCGGCTT 1242 0.500 56.7
matK-trnK-UUU_p4 matK-trnK-UUU TAGCGAAGAACTTGCACCAA ACGGTAGAGTACTCGGCTTT 1241 0.500 56.7
matK-trnK-UUU_p5 matK-trnK-UUU AGTAGCGAAGAACTTGCACC ATTTGAAGATGCGTGTGTGC 1453 0.500 55.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAGGCAGGCGTTTTTAAGGA 967–982 1.000 85.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AGGCAGGCGTTTTTAAGGAA 966–981 1.000 85.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGGCAGGCGTTTTTAAGGA 966–981 1.000 85.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGGCAGGCGTTTTTAAGGAA 965–980 1.000 85.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTTTCAGGATCAGTCGT AGGCAGGCGTTTTTAAGGAA 967–982 1.000 85.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 433–539 1.000 84.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 426–532 1.000 84.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACACCGGATCATGTCTTT GAGGTTCGAATCCTTCCGTC 447–553 1.000 83.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 435–541 1.000 83.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 436–542 1.000 83.2
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA TTATGGCCTGGTTGTAGCAC 367–377 1.000 83.9
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG TTATGGCCTGGTTGTAGCAC 368–378 1.000 83.3
atpF-atpH_p3 atpF-atpH TGGCCCAAAGAAACGAAAGA CCTGGTTGTAGCACTAGCAC 361–371 1.000 82.8
atpF-atpH_p4 atpF-atpH AGTGGCCCAAAGAAACGAAA TTATGGCCTGGTTGTAGCAC 369–379 1.000 82.5
atpF-atpH_p5 atpF-atpH GTGGCCCAAAGAAACGAAAG CCTGGTTGTAGCACTAGCAC 362–372 1.000 82.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCGAGATTTACT 811–845 1.000 85.6
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCGAGATTTACT 829–863 1.000 83.3
trnC-GCA-petN_p3 trnC-GCA-petN TTCCCTATTGTGTACCGTGC CAGCCCAAGCGAGATTTACT 874–908 1.000 82.7
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC CAGCCCAAGCGAGATTTACT 806–840 1.000 79.6
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 818–852 1.000 78.5
trnS-GGA-rps4_p1 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG ATGAATTGCTGGTGGTAGAA 261–264 1.000 57.4
trnS-GGA-rps4_p2 trnS-GGA-rps4 AGGCTTTTGTTTACCGAGGG TGAATTGCTGGTGGTAGAAT 260–263 1.000 57.4
trnS-GGA-rps4_p3 trnS-GGA-rps4 GTAGGAAAGATGGCCGAGTG AATGAATTGCTGGTGGTAGA 312–315 1.000 56.8
trnS-GGA-rps4_p4 trnS-GGA-rps4 GTAGGAAAGATGGCCGAGTG ATGAATTGCTGGTGGTAGAA 311–314 1.000 56.8
trnS-GGA-rps4_p5 trnS-GGA-rps4 GTAGGAAAGATGGCCGAGTG TGAATTGCTGGTGGTAGAAT 310–313 1.000 56.8

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
Stylidium debile MZ239203.1 150105 View on NCBI ↗
Stylidium petiolare MZ239204.1 150998 View on NCBI ↗