Markers + reference

Agenium

2 species · Poaceae · Poales

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Species 2
Genome length 138–138 kb
Candidate markers 269
Primer pairs 90

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 246 0.0041 1.00 44.5 yes View details
rps16-trnQ-UUG LSC 491 0.0020 1.00 57.7 yes View details
psbK-psbI LSC 282 0.0000 1.00 27.5 yes View details
trnS-GCU-psbD LSC 984 0.0010 1.00 59.3 yes View details
rpoA LSC 1020 0.0010 1.00 59.3 yes View details
ndhF SSC 2217 0.0014 1.00 58.0 yes View details
rpl32-trnL-UAG SSC 555 0.0036 1.00 59.9 yes View details
infA-rps8 LSC 79 0.0127 1.00 59.8 yes View details
matK-trnK-UUU LSC 696 0.0014 1.00 59.6 yes View details
trnD-GUC-psbM LSC 1057 0.0009 1.00 59.3 yes View details
trnC-GCA-rpoB LSC 1139 0.0009 1.00 59.3 yes View details
psbE-petL LSC 1295 0.0008 1.00 59.2 yes View details
rpl16 LSC 1504 0.0007 1.00 59.1 yes View details
ndhD SSC 1503 0.0007 1.00 59.1 yes View details
atpB-rbcL LSC 807 0.0000 1.00 58.9 yes View details
rbcL-psaI LSC 926 0.0000 1.00 58.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU AAGACGGTTTTCGGTGCTAG ACTCCATCCGACTAGTTCCG 380 1.000 73.7
psbA-trnK-UUU_p2 psbA-trnK-UUU AAAGACGGTTTTCGGTGCTA ACTCCATCCGACTAGTTCCG 381 1.000 73.4
psbA-trnK-UUU_p3 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT ACTCCATCCGACTAGTTCCG 382 1.000 73.4
psbA-trnK-UUU_p4 psbA-trnK-UUU AACACCGAACCATCCAATGT ACTCCATCCGACTAGTTCCG 401 1.000 73.0
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT ACTCCATCCGACTAGTTCCG 332 1.000 73.0
trnK-UUU_p1 trnK-UUU GCAAAACTCAGATTGCTCTT GAGCGTCCGGTGTAATTTCA 2656 1.000 49.7
trnK-UUU_p2 trnK-UUU GCAAAACTCAGATTGCTCTT AGCGTCCGGTGTAATTTCAT 2655 1.000 48.8
trnK-UUU_p3 trnK-UUU GCAAAACTCAGATTGCTCTTT GAGCGTCCGGTGTAATTTCA 2656 1.000 48.4
trnK-UUU_p4 trnK-UUU GCAAAACTCAGATTGCTCTT ATGTTTTGACAGGAGCGTCC 2668 1.000 48.2
trnK-UUU_p5 trnK-UUU GCAAAACTCAGATTGCTCTTT AGCGTCCGGTGTAATTTCAT 2655 1.000 47.5
matK-trnK-UUU_p1 matK-trnK-UUU CCATAATCACGAGCAAATGCA GAGCGTCCGGTGTAATTTCA 898 1.000 64.3
matK-trnK-UUU_p2 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA GAGCGTCCGGTGTAATTTCA 847 1.000 64.1
matK-trnK-UUU_p3 matK-trnK-UUU CCATAATCACGAGCAAATGCA AGCGTCCGGTGTAATTTCAT 897 1.000 63.3
matK-trnK-UUU_p4 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA AGCGTCCGGTGTAATTTCAT 846 1.000 63.1
matK-trnK-UUU_p5 matK-trnK-UUU CCATAATCACGAGCAAATGCA ATGTTTTGACAGGAGCGTCC 910 1.000 62.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 565 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 576 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 569 1.000 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 580 1.000 76.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 571 1.000 75.6
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TTTTTACTCCTCACGCCCAG 475 1.000 78.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCACGCCCAG 426 1.000 78.1
psbK-psbI_p3 psbK-psbI ACCCGAAGCTTATGCCATTT TTTTTACTCCTCACGCCCAG 505 1.000 77.4
psbK-psbI_p4 psbK-psbI TTAGCGTTTGTTTGGCAAGC TTTTTACTCCTCACGCCCAG 435 1.000 77.3
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTACTCCTCACGCCCAG 423 1.000 76.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1133 1.000 79.0
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1132 1.000 78.7
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1129 1.000 78.4
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1116 1.000 77.8
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ATAAGCCGGACCATCCTACA 1119 1.000 76.0

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
Agenium leptocladum NC_059819.1 137726 View on NCBI ↗
Agenium villosum NC_059820.1 137731 View on NCBI ↗