Markers + reference

Enneapogon

2 species · Poaceae · Poales

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Species 2
Genome length 133–133 kb
Candidate markers 262
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 8 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 518 0.0154 1.00 62.2 yes View details
rps16-trnQ-UUG LSC 508 0.0139 0.99 59.8 yes View details
trnG-GCC-trnfM-CAU LSC 355 0.0171 0.99 64.5 yes View details
trnY-GUA-trnD-GUC LSC 385 0.0111 0.94 58.9 yes View details
atpF LSC 1393 0.0065 1.00 57.3 yes View details
trnF-GAA-ndhJ LSC 546 0.0128 1.00 65.2 yes View details
petA LSC 963 0.0010 1.00 57.6 yes View details
petA-psbJ LSC 746 0.0148 0.99 67.8 yes View details
psbE-petL LSC 1310 0.0054 0.99 59.4 yes View details
ndhG SSC 531 0.0019 1.00 44.7 yes View details
ndhG-ndhI SSC 215 0.0233 1.00 65.9 yes View details
petN-trnC-GCA LSC 861 0.0058 1.00 62.6 yes View details
rps18-rpl20 LSC 238 0.0129 0.97 62.3 yes View details
trnE-UUC-trnY-GUA LSC 61 0.0328 1.00 61.8 yes View details
trnS-GCU-psbD LSC 871 0.0023 0.98 61.6 yes View details
atpH-atpF LSC 450 0.0090 0.99 61.6 yes View details
trnG-UCC-trnT-GGU LSC 984 0.0031 1.00 60.9 yes View details
rps8-rpl14 LSC 140 0.0143 1.00 60.7 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_p1 trnK-UUU ATACCAGTGTCAACCAAGCC ACTTCGCTCAATTGCTAGGG 2971–2982 1.000 78.7
trnK-UUU_p2 trnK-UUU ATACCAGTGTCAACCAAGCC CTTCGCTCAATTGCTAGGGT 2970–2981 1.000 78.7
trnK-UUU_p3 trnK-UUU ATACCAGTGTCAACCAAGCC GGAGGGTCCGGTGTAATTTC 2743–2754 1.000 78.6
trnK-UUU_p4 trnK-UUU CAAGCCAACCCAAACGATTG ACTTCGCTCAATTGCTAGGG 2957–2968 1.000 78.6
trnK-UUU_p5 trnK-UUU CAAGCCAACCCAAACGATTG CTTCGCTCAATTGCTAGGGT 2956–2967 1.000 78.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GCTCAACCCACAAGAACTGT 641 1.000 73.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GTGCTCAACCCACAAGAACT 643 1.000 73.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TGCTCAACCCACAAGAACTG 642 1.000 73.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GCTCAACCCACAAGAACTGT 639 1.000 72.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GTGCTCAACCCACAAGAACT 641 1.000 72.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 577–581 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 588–592 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 581–585 1.000 75.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 589–593 1.000 74.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 569–573 1.000 74.6
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1002–1016 1.000 79.6
trnS-GCU-psbD_p2 trnS-GCU-psbD TCGAAAGTCCCAAACGATCC GCCGGACCATCCTACAAAAA 1077–1091 1.000 79.1
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 989–1003 1.000 79.0
trnS-GCU-psbD_p4 trnS-GCU-psbD TCGAAAGTCCCAAACGATCC ACAAAAACGAAACGGTCCCT 1064–1078 1.000 78.5
trnS-GCU-psbD_p5 trnS-GCU-psbD CGAAAGTCCCAAACGATCCA GCCGGACCATCCTACAAAAA 1076–1090 1.000 78.2
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC AGTTTTTGGCCCTACAGAGC 473–477 1.000 80.4
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA AGTTTTTGGCCCTACAGAGC 513–517 1.000 80.2
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GACCCAGGCGGATATATCCT AGTTTTTGGCCCTACAGAGC 550–554 1.000 79.7
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT AGTTTTTGGCCCTACAGAGC 517–521 1.000 79.4
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU ATATAGGACGTAGCGAGCGT AGTTTTTGGCCCTACAGAGC 525–529 1.000 79.3
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTCTGTCTTGC 1135–1138 1.000 51.5
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC ACCGATGACTTCTGTCTTGC 1138–1141 1.000 50.5
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACCGATGACTTCTGTCTTGC 1137–1140 1.000 50.5
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AACGAATCACACTTTTACCACT ACCGATGACTTCTGTCTTGC 1136–1139 1.000 49.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU TACCACTAAACTATACCCGC ACCGATGACTTCTGTCTTGC 1121–1124 1.000 47.7

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
Enneapogon caerulescens NC_042837.1 133231 View on NCBI ↗
Enneapogon oblongus NC_036682.1 133433 View on NCBI ↗