Markers + reference

Chasmanthium

2 species · Poaceae · Poales

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Species 2
Genome length 141–141 kb
Candidate markers 265
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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-trnfM-CAU LSC 376 0.0275 0.97 65.2 yes View details
petN-trnC-GCA LSC 919 0.0022 0.97 60.3 yes View details
ndhC-trnV-UAC LSC 984 0.0031 0.98 62.7 yes View details
rpl16 LSC 1477 0.0020 1.00 60.3 yes View details
rps15-ndhF IRb 415 0.0000 0.34 33.6 yes View details
ndhF-rpl32 SSC 828 0.0036 1.00 60.8 yes View details
ndhH SSC 1182 0.0059 1.00 62.2 yes View details
matK-trnK-UUU LSC 672 0.0074 1.00 61.4 yes View details
clpP-psbB LSC 528 0.0000 0.96 60.9 yes View details
rbcL-psaI LSC 934 0.0032 1.00 60.6 yes View details
atpI-atpH LSC 835 0.0012 0.99 60.3 yes View details
atpB-rbcL LSC 796 0.0025 1.00 60.3 yes View details
petD LSC 1223 0.0025 1.00 60.2 yes View details
psbM-petN LSC 801 0.0013 0.99 60.1 yes View details
petA-psbJ LSC 901 0.0022 1.00 60.0 yes View details
trnD-GUC-psbM LSC 1056 0.0019 1.00 59.9 yes View details
trnG-UCC-trnT-GGU LSC 1813 0.0011 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TCAAAACTCCGATTGCTCTT TTCAATGTTTTGACAGGCGC 2640–2660 1.000 57.4
trnK-UUU_p2 trnK-UUU TTCAAAACTCCGATTGCTCT TTCAATGTTTTGACAGGCGC 2641–2661 1.000 57.4
trnK-UUU_p3 trnK-UUU TCAAAACTCCGATTGCTCTTT TTCAATGTTTTGACAGGCGC 2640–2660 1.000 55.8
trnK-UUU_p4 trnK-UUU TTCAAAACTCCGATTGCTCTT TTCAATGTTTTGACAGGCGC 2641–2661 1.000 55.8
trnK-UUU_p5 trnK-UUU ATTCAAAACTCCGATTGCTCT TTCAATGTTTTGACAGGCGC 2642–2662 1.000 54.0
matK-trnK-UUU_p1 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT TTCAATGTTTTGACAGGCGC 859–879 1.000 63.2
matK-trnK-UUU_p2 matK-trnK-UUU ATTCCTGAAAGAGAAGTGGGT TTCAATGTTTTGACAGGCGC 860–880 1.000 59.7
matK-trnK-UUU_p3 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT GTCCGGTGTAATTCCATCGA 839–859 1.000 59.6
matK-trnK-UUU_p4 matK-trnK-UUU TGAAAGAGAAGTGGGTAAACGA TTCAATGTTTTGACAGGCGC 855–875 1.000 58.0
matK-trnK-UUU_p5 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT CGTCCGGTGTAATTCCATCG 840–860 1.000 57.9
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU CCGTAGCAAGCGTAGTTCAA CGAGGCTCATAACCTTGAGG 506–518 1.000 79.2
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU CCGTAGCAAGCGTAGTTCAA CAGTTTGGTAGCTCACGAGG 521–533 1.000 78.7
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU CCGTAGCAAGCGTAGTTCAA CAGTTTTCGGCCCTACAGAG 551–563 1.000 78.6
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU CCGTAGCAAGCGTAGTTCAA CTACAGAGCGGAGTAGAGCA 539–551 1.000 78.2
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU CCGTAGCAAGCGTAGTTCAA TACAGAGCGGAGTAGAGCAG 538–550 1.000 78.2
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTAAGTGAAAAGCCCT 1913–1933 1.000 41.8
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1883–1903 1.000 41.7
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTCTGTCTTACCAAGGCA 1941–1961 1.000 41.4
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTCTGTCTTACCAAGGC 1942–1962 1.000 41.4
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1879–1899 1.000 40.9
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTT 1220–1221 1.000 66.0
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AATCATTTTGGCTGGCTGTT 1222–1223 1.000 64.1
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATCATTTTGGCTGGCTGTTT 1221–1222 1.000 64.1
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTTT 1220–1221 1.000 63.9
trnD-GUC-psbM_p5 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TTTGGCTGGCTGTTTTTACA 1216–1217 1.000 63.2
psbM-petN_p1 psbM-petN AAAACAGCCAGCCAAAATGA TAGTAAGTCTCGCTTGGGCT 903–908 1.000 68.9
psbM-petN_p2 psbM-petN AAAACAGCCAGCCAAAATGA GTAGTATGGGGGAGGAGTGG 847–852 1.000 67.9
psbM-petN_p3 psbM-petN AAAACAGCCAGCCAAAATGA TAGTATGGGGGAGGAGTGGA 846–851 1.000 67.2
psbM-petN_p4 psbM-petN AAACAGCCAGCCAAAATGAT TAGTAAGTCTCGCTTGGGCT 902–907 1.000 67.1
psbM-petN_p5 psbM-petN AACAGCCAGCCAAAATGATT TAGTAAGTCTCGCTTGGGCT 901–906 1.000 67.1

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
Chasmanthium laxum NC_035522.1 141203 View on NCBI ↗
Chasmanthium laxum subsp. sessiliflorum KU291494.1 140892 View on NCBI ↗