Markers + reference

Chrysopogon

4 species · Poaceae · Poales

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Species 4
Genome length 140–141 kb
Candidate markers 288
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 288 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1092 0.0096 1.00 53.4 yes View details
trnG-UCC-trnT-GGU LSC 1958 0.0114 1.00 59.8 yes View details
trnT-GGU-trnM-CAU LSC 397 0.0333 0.83 64.0 yes View details
trnC-GCA-rpoB LSC 1207 0.0106 1.00 65.3 yes View details
trnF-GAA-ndhJ LSC 581 0.0100 0.96 58.0 yes View details
ndhC-trnV-UAC LSC 979 0.0089 0.98 57.6 yes View details
rbcL-psaI LSC 932 0.0145 1.00 54.0 yes View details
petA-psbJ LSC 890 0.0150 1.00 55.6 yes View details
ndhF-rpl32 SSC 821 0.0116 1.00 61.1 yes View details
rpl32-trnL-UAG SSC 528 0.0224 1.00 64.1 yes View details
ccsA SSC 966 0.0072 1.00 53.6 yes View details
ndhA SSC 2127 0.0090 1.00 53.4 yes View details
atpI-atpH LSC 799 0.0111 1.00 68.6 yes View details
trnV-UAC-trnM-CAU LSC 214 0.0210 1.00 65.6 yes View details
ycf3-trnS-GGA LSC 590 0.0065 1.00 64.3 yes View details
psaA-ycf3 LSC 600 0.0075 1.00 64.0 yes View details
ycf4-cemA LSC 372 0.0112 1.00 63.3 yes View details
atpF LSC 1383 0.0057 1.00 62.3 yes View details
rps4-trnT-UGU LSC 319 0.0047 0.94 60.9 yes View details
psbM-petN LSC 816 0.0113 0.99 59.8 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_p1 rps16 TGAGGATCAGTCGTGGTCTT ATCTTTGCAGAGTGTTCCCC 1941–1953 1.000 79.9
rps16_p2 rps16 AGGATCAGTCGTGGTCTTCT ATCTTTGCAGAGTGTTCCCC 1939–1951 1.000 78.7
rps16_p3 rps16 TGAGGATCAGTCGTGGTCTT ACCCCAAAACGACCAATCTT 2226–2237 1.000 78.6
rps16_p4 rps16 TGAGGATCAGTCGTGGTCTT GCAGAGTGTTCCCCGATAAA 1935–1947 1.000 78.4
rps16_p5 rps16 TGAAATTACACCGGACGCTC ATCTTTGCAGAGTGTTCCCC 1771–1783 1.000 78.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2074–2117 1.000 43.5
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2044–2087 1.000 43.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 2040–2083 1.000 42.6
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 2041–2084 1.000 42.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 2076–2119 1.000 42.5
trnT-GGU-trnM-CAU_p1 trnT-GGU-trnM-CAU AAAAATGGAACTTCCGGGCT GCATCGACCCAGGAAGAATT 1106–1169 1.000 86.6
trnT-GGU-trnM-CAU_p2 trnT-GGU-trnM-CAU AAAATGGAACTTCCGGGCTT GCATCGACCCAGGAAGAATT 1105–1168 1.000 86.6
trnT-GGU-trnM-CAU_p3 trnT-GGU-trnM-CAU AAATGGAACTTCCGGGCTTT GCATCGACCCAGGAAGAATT 1104–1167 1.000 86.6
trnT-GGU-trnM-CAU_p4 trnT-GGU-trnM-CAU GGCCCATTGTTGTATCCGAT GCATCGACCCAGGAAGAATT 1163–1226 1.000 86.6
trnT-GGU-trnM-CAU_p5 trnT-GGU-trnM-CAU AAGTCATCGGTTCGAATC ACTATAATGATAGTATGAGCAGT 389–459 1.000 49.1
psbM-petN_p1 psbM-petN TGTTCATTCTAGTTCCTACTGCC TAGTAAGTCTCGCTTGGGCT 961–968 1.000 56.3
psbM-petN_p2 psbM-petN TGTTCATTCTAGTTCCTACTGCC GTAGTATGGGGGAGGAGTGG 905–912 1.000 55.3
psbM-petN_p3 psbM-petN TGTTCATTCTAGTTCCTACTGCC TAGTATGGGGGAGGAGTGGA 904–911 1.000 54.6
psbM-petN_p4 psbM-petN GTTCATTCTAGTTCCTACTGCCT TAGTAAGTCTCGCTTGGGCT 960–967 1.000 54.2
psbM-petN_p5 psbM-petN TGTTCATTCTAGTTCCTACTGCC CGCTAGTAGTATGGGGGAGG 910–917 1.000 54.0
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CTTCTCAAGTTCTTCCGCCA 1337–1377 1.000 82.2
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TCTCAAGTTCTTCCGCCAAG 1335–1375 1.000 82.2
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG ACTTCTCAAGTTCTTCCGCC 1338–1378 1.000 82.2
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG TTCCGCCAAGCCTTGATTAA 1325–1365 1.000 81.9
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CTTCCGCCAAGCCTTGATTA 1326–1366 1.000 81.6
atpI-atpH_p1 atpI-atpH TAGCCGCAGCCTATATAGGT CAGTACCTTGACCAACTCCG 927–952 1.000 77.9
atpI-atpH_p2 atpI-atpH ATTTTTGCAACGTTAGCCGC CAGTACCTTGACCAACTCCG 940–965 1.000 77.4
atpI-atpH_p3 atpI-atpH TAGCCGCAGCCTATATAGGT AAGCAGCAGCAATTAGTGGA 861–886 1.000 77.2
atpI-atpH_p4 atpI-atpH TAGCCGCAGCCTATATAGGT GCAGTACCTTGACCAACTCC 928–953 1.000 77.1
atpI-atpH_p5 atpI-atpH TAGCCGCAGCCTATATAGGT GCCAATCCAGCAGCAATAAC 883–908 1.000 77.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Chrysopogon aciculatus NC_046489.1 140696 View on NCBI ↗
Chrysopogon gryllus NC_035035.1 140034 View on NCBI ↗
Chrysopogon orientalis NC_035047.1 140712 View on NCBI ↗
Chrysopogon zizanioides NC_035034.1 139971 View on NCBI ↗