Markers + reference

Amphipogon

2 species · Poaceae · Poales

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Species 2
Genome length 136–136 kb
Candidate markers 265
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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 560 0.0403 0.97 71.5 yes View details
rps16-trnQ-UUG LSC 1137 0.0309 0.71 65.3 yes View details
trnG-UCC-trnT-GGU LSC 1683 0.0419 0.96 75.1 yes View details
trnD-GUC-psbM LSC 1049 0.0417 0.53 61.8 yes View details
psaA-ycf3 LSC 635 0.0394 1.00 75.6 yes View details
ndhC-trnV-UAC LSC 910 0.0291 0.98 66.1 yes View details
rbcL-psaI LSC 888 0.0390 0.98 68.2 yes View details
ndhF-rpl32 SSC 854 0.0544 0.93 78.0 yes View details
ccsA SSC 924 0.0097 1.00 50.5 yes View details
rps14-psaB LSC 154 0.0458 0.99 79.4 yes View details
ndhH-rps15 IRa 126 0.0661 0.96 79.4 yes View details
rps15-ndhF IRb 108 0.0680 0.95 74.2 yes View details
ccsA-ndhD SSC 190 0.0842 1.00 73.2 yes View details
rpl14-rpl16 LSC 106 0.0485 0.97 72.3 yes View details
rps11-rpl36 LSC 173 0.0533 0.98 69.9 yes View details
cemA-petA LSC 228 0.0307 1.00 69.4 yes View details
psbE-petL LSC 1051 0.0236 0.97 69.0 yes View details
rps19-psbA LSC 124 0.0565 1.00 68.2 no View details
atpI-atpH LSC 805 0.0276 0.99 68.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AGAAAAAGAAAGAGCTTTGAGT 638 0.500 20.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA AGAAAAAGAAAGAGCTTTGAGT 639 0.500 20.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA AGAAAAAGAAAGAGCTTTGAGT 636 0.500 20.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AGAAAGAAAAAGAAAGAGCTTTGAGT 642 0.500 20.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AGAAAAAGAAAGAGCTTTGAGTT 638 0.500 20.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 883–1211 1.000 84.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCACTCGGAGGTTCGAATC 891–1219 1.000 84.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 894–1222 1.000 83.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTCACTCGGAGGTTCGAATC 902–1230 1.000 83.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 887–1215 1.000 83.1
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1729–1773 1.000 46.6
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1725–1769 1.000 45.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1726–1770 1.000 45.9
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 1732–1776 1.000 45.9
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1731–1775 1.000 45.9
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 676–1134 1.000 54.1
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 677–1135 1.000 51.0
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 676–1134 1.000 51.0
trnD-GUC-psbM_p4 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 677–1135 1.000 49.9
trnD-GUC-psbM_p5 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AATGCGAGAATATTGACTTCCA 678–1136 1.000 49.2
atpI-atpH_p1 atpI-atpH TAGCCGCAGCCTATATAGGT AGCCAATCCAGCAGCAATAA 897–899 1.000 77.4
atpI-atpH_p2 atpI-atpH TAGCCGCAGCCTATATAGGT AAGCAGCAGCAATTAGTGGA 874–876 1.000 77.0
atpI-atpH_p3 atpI-atpH TAGCCGCAGCCTATATAGGT GCAGTACCTTGACCAACTCC 941–943 1.000 76.9
atpI-atpH_p4 atpI-atpH ATTTTTGCAACGTTAGCCGC AGCCAATCCAGCAGCAATAA 910–912 1.000 76.8
atpI-atpH_p5 atpI-atpH TAGCCGCAGCCTATATAGGT GCCAATCCAGCAGCAATAAC 896–898 1.000 76.8
rps14-psaB_p1 rps14-psaB ATTTCTGCCGCTTCTTCTCC GCTCACTTTTCCGTGGGTTA 275 1.000 79.4
rps14-psaB_p2 rps14-psaB ATTTCTGCCGCTTCTTCTCC TTAGCTCACTTTTCCGTGGG 278 1.000 78.8
rps14-psaB_p3 rps14-psaB ATTTCTGCCGCTTCTTCTCC GCAGCTTTCTTGATTGCCTC 242 1.000 78.4
rps14-psaB_p4 rps14-psaB ATTTCTGCCGCTTCTTCTCC GCTCTTTCCATTGTGCAAGC 311 1.000 77.7
rps14-psaB_p5 rps14-psaB ATTTCTGCCGCTTCTTCTCC TGGCTCTTTCCATTGTGCAA 313 1.000 77.6

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
Amphipogon caricinus NC_035520.1 135994 View on NCBI ↗
Amphipogon turbinatus NC_035521.1 135638 View on NCBI ↗