Markers + reference

Dichanthelium

6 species · Poaceae · Poales

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Species 6
Genome length 140–140 kb
Candidate markers 269
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1200 0.0055 1.00 63.8 yes View details
trnG-UCC-trnM-CAU LSC 1961 0.0039 1.00 59.3 yes View details
trnT-UGU-trnL-UAA LSC 834 0.0084 1.00 69.0 yes View details
trnF-GAA-ndhJ LSC 563 0.0094 1.00 57.0 yes View details
ndhC-trnV-UAC LSC 930 0.0052 1.00 54.6 yes View details
rbcL LSC 1431 0.0042 1.00 45.8 yes View details
rbcL-psaI LSC 1000 0.0063 0.97 47.2 yes View details
petA-psbJ LSC 898 0.0079 1.00 48.3 yes View details
ndhF-rpl32 SSC 840 0.0058 1.00 58.8 yes View details
rpl32-trnL-UAG SSC 533 0.0091 1.00 46.6 yes View details
trnS-GCU-psbD LSC 996 0.0026 1.00 61.8 yes View details
trnC-GCA-rpoB LSC 1170 0.0037 1.00 56.5 yes View details
rpl16 LSC 1503 0.0023 1.00 52.2 yes View details
atpF LSC 1388 0.0012 1.00 52.0 yes View details
psbE-petL LSC 1287 0.0016 1.00 51.8 yes View details
psaA LSC 2253 0.0016 1.00 51.7 yes View details
trnG-GCC-trnfM-CAU LSC 337 0.0032 0.98 51.4 yes View details
trnT-GGU-trnE-UUC LSC 461 0.0026 1.00 51.4 yes View details
ycf4-cemA LSC 363 0.0035 0.99 51.4 yes View details
petN-trnC-GCA LSC 931 0.0029 1.00 51.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1270–1282 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1281–1293 1.000 79.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1274–1286 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1285–1297 1.000 78.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1276–1288 1.000 77.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1118–1142 1.000 81.4
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1105–1129 1.000 80.8
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1104–1128 1.000 78.4
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1097–1121 1.000 78.2
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1091–1115 1.000 77.9
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT CGAGGCTCATAACCTTGAGG 443–479 1.000 81.1
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU ATATAGGACGTAGCGAGCGT CGAGGCTCATAACCTTGAGG 451–487 1.000 80.9
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT CAGTTTGGTAGCTCACGAGG 458–494 1.000 80.6
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU ATATAGGACGTAGCGAGCGT CAGTTTGGTAGCTCACGAGG 466–502 1.000 80.5
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT TACAGAGCGGAGTAGAGCAG 475–511 1.000 80.3
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2046–2080 1.000 43.1
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2016–2050 1.000 42.9
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 2012–2046 1.000 42.2
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 2013–2047 1.000 42.2
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2048–2082 1.000 42.2
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGGGCTTTTCACTTAGTGGT GCTGCCTCCTTGAAAGAGAG 571–578 1.000 69.2
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGGGCTTTTCACTTAGTGGT TGTCCTGAACCACTAGACGA 550–557 1.000 69.1
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 601–608 1.000 68.9
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 580–587 1.000 68.8
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GTCATCAGTTCGAATCCGAGA GCTGCCTCCTTGAAAGAGAG 526–533 1.000 68.8
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CTGCAAATCCTTTACCCCCA 993–999 1.000 78.4
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TGCAAATCCTTTACCCCCAG 992–998 1.000 78.4
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA ACTGCAAATCCTTTACCCCC 994–1000 1.000 78.4
petN-trnC-GCA_p4 petN-trnC-GCA AGCCCAAGCGAGACTTACTA GCAAATCCTTTACCCCCAGT 991–997 1.000 78.4
petN-trnC-GCA_p5 petN-trnC-GCA CCACTCCTCCCCCATACTAC TGCAAATCCTTTACCCCCAG 1048–1054 1.000 77.3

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
Dichanthelium acuminatum NC_030623.1 140122 View on NCBI ↗
Dichanthelium boreale NC_050413.1 140089 View on NCBI ↗
Dichanthelium commutatum NC_050414.1 139591 View on NCBI ↗
Dichanthelium dichotomum NC_050411.1 140105 View on NCBI ↗
Dichanthelium portoricense NC_050412.1 140107 View on NCBI ↗
Dichanthelium ravenelii NC_050403.1 140063 View on NCBI ↗