Markers + reference

Pleioblastus

9 species · Poaceae · Poales

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Species 9
Genome length 139–140 kb
Candidate markers 268
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnT-GGU LSC 1998 0.0033 0.65 34.6 yes View details
rbcL LSC 1434 0.0028 1.00 36.3 yes View details
rbcL-psaI LSC 1292 0.0047 1.00 32.1 yes View details
clpP LSC 651 0.0053 1.00 48.1 yes View details
psbB-psbT LSC 170 0.0000 1.00 19.6 yes View details
ndhF-rpl32 SSC 865 0.0031 1.00 53.1 yes View details
ndhG SSC 531 0.0010 1.00 27.3 yes View details
ndhG-ndhI SSC 246 0.0149 1.00 48.4 yes View details
ndhA SSC 2115 0.0028 1.00 47.6 yes View details
psbT-psbN LSC 48 0.0579 1.00 60.9 yes View details
rpl32-trnL-UAG SSC 728 0.0037 0.97 52.0 yes View details
trnT-UGU-trnL-UAA LSC 825 0.0014 0.99 48.3 yes View details
rpoC2-rps2 LSC 322 0.0043 0.94 46.0 yes View details
trnS-GCU-psbD LSC 974 0.0007 0.99 45.7 yes View details
psbA LSC 1062 0.0009 1.00 44.9 yes View details
ndhC-trnV-UAC LSC 744 0.0018 1.00 43.4 yes View details
atpB-rbcL LSC 781 0.0010 1.00 43.1 yes View details
psbE-petL LSC 1228 0.0013 1.00 43.1 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_p1 psbA TCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1159 1.000 68.7
psbA_p2 psbA TTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1160 1.000 68.7
psbA_p3 psbA TCTGGCTTTCCTTCCTTCAAA AATACGTGTGCTTGGGAGTC 1159 1.000 66.7
psbA_p4 psbA TTCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1160 1.000 66.7
psbA_p5 psbA TTTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1161 1.000 66.7
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1119–1137 1.000 79.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1106–1124 1.000 78.6
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1105–1123 1.000 76.2
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1098–1116 1.000 76.0
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1092–1110 1.000 75.6
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1390–2085 1.000 45.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1386–2081 1.000 45.0
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1387–2082 1.000 45.0
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 1393–2088 1.000 45.0
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1392–2087 1.000 45.0
rpoC2-rps2_p1 rpoC2-rps2 ATGAGACATCAGAACCCCCA ACCAAAATGAACTCCCGCTT 408–429 1.000 84.5
rpoC2-rps2_p2 rpoC2-rps2 TGAGACATCAGAACCCCCAT ACCAAAATGAACTCCCGCTT 407–428 1.000 84.5
rpoC2-rps2_p3 rpoC2-rps2 ATGAGACATCAGAACCCCCA TTTACGCTTTGCCGAGATGT 465–486 1.000 82.6
rpoC2-rps2_p4 rpoC2-rps2 TGAGACATCAGAACCCCCAT TTTACGCTTTGCCGAGATGT 464–485 1.000 82.6
rpoC2-rps2_p5 rpoC2-rps2 TGAGACATCAGAACCCCCAT CTTTGCCGAGATGTAAGGGG 458–479 1.000 81.6
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG ACAATCAAGTCCGTAGCGTC 917–928 1.000 80.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA CGATGACCCTCGCATTACAA ACAATCAAGTCCGTAGCGTC 909–920 1.000 80.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACAATCAAGTCCGTAGCGTC 887–898 1.000 79.9
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG CCGTAGCGTCTACCGATTTC 907–918 1.000 78.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG CAATCAAGTCCGTAGCGTCT 916–927 1.000 78.6
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCCTTCACTAATCGGGGCTA GGTTCGAATCCGTATAGCCC 877 1.000 75.9
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CTGGTCCTTCACTAATCGGG GGTTCGAATCCGTATAGCCC 881 1.000 74.8
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCCTTCACTAATCGGGGCTA CGGTTCGAATCCGTATAGCC 878 1.000 74.1
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TGGTCCTTCACTAATCGGGG GGTTCGAATCCGTATAGCCC 880 1.000 73.3
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CTGGTCCTTCACTAATCGGG CGGTTCGAATCCGTATAGCC 882 1.000 73.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Pleioblastus amarus NC_043892.1 139703 View on NCBI ↗
Pleioblastus argenteostriatus NC_069216.1 139031 View on NCBI ↗
Pleioblastus chino PQ636882.1 139067 View on NCBI ↗
Pleioblastus gramineus PQ472931.1 139061 View on NCBI ↗
Pleioblastus maculatus NC_024723.1 139720 View on NCBI ↗
Pleioblastus ovatoauritus NC_069220.1 139708 View on NCBI ↗
Pleioblastus simonii PQ472933.1 139093 View on NCBI ↗
Pleioblastus triangulata NC_067033.1 139690 View on NCBI ↗
Pleioblastus variegatus NC_069217.1 139067 View on NCBI ↗