Markers + reference

Trichoneura

6 species · Poaceae · Poales

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Species 6
Genome length 134–135 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 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
rps16 LSC 1097 0.0046 1.00 49.9 yes View details
rps16-trnQ-UUG LSC 1264 0.0049 1.00 60.5 yes View details
trnS-GCU-psbD LSC 962 0.0057 1.00 58.2 yes View details
trnG-GCC-trnG-UCC LSC 537 0.0065 1.00 53.7 yes View details
trnG-UCC-trnE-UUC LSC 1606 0.0057 0.98 58.0 yes View details
trnY-GUA-trnD-GUC LSC 351 0.0114 1.00 49.9 yes View details
trnT-UGU-trnL-UAA LSC 827 0.0074 0.97 60.5 yes View details
psbE-petL LSC 1320 0.0050 1.00 56.2 yes View details
rpl16 LSC 1497 0.0069 0.97 57.3 yes View details
ndhF-rpl32 SSC 891 0.0067 1.00 53.0 yes View details
rpl32-trnL-UAG SSC 412 0.0162 1.00 70.6 yes View details
psaA-ycf3 LSC 676 0.0044 0.99 63.0 yes View details
trnC-GCA-rpoB LSC 999 0.0034 0.99 61.9 yes View details
petN-trnC-GCA LSC 732 0.0051 1.00 60.4 yes View details
ndhA SSC 2092 0.0019 1.00 59.2 yes View details
ycf3-trnS-GGA LSC 579 0.0048 1.00 58.5 yes View details
ndhD SSC 1503 0.0024 1.00 58.5 yes View details
atpI-atpH LSC 807 0.0031 1.00 56.4 yes View details
atpB-rbcL LSC 803 0.0041 1.00 56.2 yes View details
trnF-GAA-ndhJ LSC 550 0.0036 1.00 55.4 yes View details
trnP-UGG-psaJ LSC 406 0.0016 1.00 55.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 AGGGATATTAATGAACCTCCCT CACTTTGCAATGAAATTAGAGGA 1174–1182 1.000 41.0
rps16_p2 rps16 TGAACCTCCCTTACTTTTTCA CACTTTGCAATGAAATTAGAGGA 1163–1171 1.000 41.0
rps16_p3 rps16 AAGGGATATTAATGAACCTCCCT CACTTTGCAATGAAATTAGAGGA 1175–1183 1.000 41.0
rps16_p4 rps16 AGGGATATTAATGAACCTCCCTT CACTTTGCAATGAAATTAGAGGA 1174–1182 1.000 41.0
rps16_p5 rps16 AGGGATATTAATGAACCTCCCT CACTTTGCAATGAAATTAGAGGAA 1174–1182 1.000 41.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1336–1353 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1347–1364 1.000 78.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1340–1357 1.000 75.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1328–1345 1.000 74.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1335–1352 1.000 74.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1106–1113 1.000 79.6
trnS-GCU-psbD_p2 trnS-GCU-psbD GAAAGTCCCAAACGATCCGA GCCGGACCATCCTACAAAAA 1179–1186 1.000 79.1
trnS-GCU-psbD_p3 trnS-GCU-psbD TCGAAAGTCCCAAACGATCC GCCGGACCATCCTACAAAAA 1181–1188 1.000 79.1
trnS-GCU-psbD_p4 trnS-GCU-psbD AAAGTCCCAAACGATCCGAG GCCGGACCATCCTACAAAAA 1178–1185 1.000 79.0
trnS-GCU-psbD_p5 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1093–1100 1.000 79.0
trnG-GCC-trnG-UCC_p1 trnG-GCC-trnG-UCC GAAGGTACGGGTTCGATTCC AGCCTTCCAAGCTAACGATG 609–619 1.000 81.4
trnG-GCC-trnG-UCC_p2 trnG-GCC-trnG-UCC GCGAGCGTAGTTCAATGGTA AGCCTTCCAAGCTAACGATG 649–659 1.000 81.2
trnG-GCC-trnG-UCC_p3 trnG-GCC-trnG-UCC GAAGGTACGGGTTCGATTCC CCTAGCCTTCCAAGCTAACG 612–622 1.000 81.2
trnG-GCC-trnG-UCC_p4 trnG-GCC-trnG-UCC GCGAGCGTAGTTCAATGGTA CCTAGCCTTCCAAGCTAACG 652–662 1.000 80.9
trnG-GCC-trnG-UCC_p5 trnG-GCC-trnG-UCC CGTAGCGAGCGTAGTTCAAT AGCCTTCCAAGCTAACGATG 653–663 1.000 80.4
trnG-UCC-trnE-UUC_p1 trnG-UCC-trnE-UUC ACGAATCACACTTTTACCACT GCTGCCTCCTTGAAAGAGAG 1661–1688 1.000 52.3
trnG-UCC-trnE-UUC_p2 trnG-UCC-trnE-UUC ACGAATCACACTTTTACCACT TGTCCTGAACCACTAGACGA 1640–1667 1.000 52.2
trnG-UCC-trnE-UUC_p3 trnG-UCC-trnE-UUC AGAACGAATCACACTTTTACCAC GCTGCCTCCTTGAAAGAGAG 1664–1691 1.000 51.3
trnG-UCC-trnE-UUC_p4 trnG-UCC-trnE-UUC GAACGAATCACACTTTTACCACT GCTGCCTCCTTGAAAGAGAG 1663–1690 1.000 51.3
trnG-UCC-trnE-UUC_p5 trnG-UCC-trnE-UUC GAACGAATCACACTTTTACCACT TGTCCTGAACCACTAGACGA 1642–1669 1.000 51.2
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GCGGTGCTCTAACCAATTGA 476 1.000 77.3
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG GCGGTGCTCTAACCAATTGA 443 1.000 74.9
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT GCGGTGCTCTAACCAATTGA 442 1.000 74.8
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGCGGTGCTCTAACCAATT 477 1.000 72.6
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC GCGGTGCTCTAACCAATTGA 444 1.000 71.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Trichoneura eleusinoides NC_082215.1 135069 View on NCBI ↗
Trichoneura grandiglumis NC_036707.1 134286 View on NCBI ↗
Trichoneura lindleyana NC_082216.1 134347 View on NCBI ↗
Trichoneura mollis NC_082217.1 134249 View on NCBI ↗
Trichoneura schlechteri NC_082218.1 134139 View on NCBI ↗
Trichoneura weberbaueri NC_082219.1 134340 View on NCBI ↗