Markers + reference

Sinobambusa

7 species · Poaceae · Poales

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Species 7
Genome length 140–140 kb
Candidate markers 263
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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 564 0.0020 1.00 40.6 yes View details
trnG-UCC-trnT-GGU LSC 1996 0.0009 1.00 46.5 yes View details
rbcL LSC 1434 0.0019 1.00 46.0 yes View details
clpP LSC 651 0.0018 1.00 44.2 yes View details
rpl32-trnL-UAG SSC 703 0.0027 1.00 41.9 yes View details
ccsA SSC 993 0.0015 1.00 33.3 yes View details
ndhG-ndhI SSC 246 0.0093 1.00 44.7 yes View details
trnT-UGU-trnL-UAA LSC 858 0.0000 0.97 50.4 yes View details
infA LSC 342 0.0010 1.00 46.8 yes View details
trnF-GAA-ndhJ LSC 581 0.0010 1.00 45.8 yes View details
psbM-petN LSC 754 0.0008 1.00 43.4 yes View details
ndhC-trnV-UAC LSC 744 0.0008 1.00 43.4 yes View details
trnD-GUC-psbM LSC 987 0.0006 1.00 43.3 yes View details
petB LSC 1465 0.0004 1.00 43.3 yes View details
matK-trnK-UUU LSC 685 0.0000 1.00 43.0 yes View details
atpI-atpH LSC 830 0.0003 1.00 43.0 yes View details
psaA-ycf3 LSC 804 0.0004 1.00 43.0 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 AAGCCAGCCCCAACGATT CGTGCGGTGTAATTCCATTG 2740–2742 1.000 50.3
trnK-UUU_p2 trnK-UUU AAGCCAGCCCCAACGATTG CGTGCGGTGTAATTCCATTG 2740–2742 1.000 46.9
trnK-UUU_p3 trnK-UUU CAAGCCAGCCCCAACGATT CGTGCGGTGTAATTCCATTG 2741–2743 1.000 46.9
trnK-UUU_p4 trnK-UUU CAAGCCAGCCCCAACGATTG CGTGCGGTGTAATTCCATTG 2741–2743 1.000 45.0
trnK-UUU_p5 trnK-UUU AGCCAGCCCCAACGATTG CGTGCGGTGTAATTCCATTG 2739–2741 1.000 43.9
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 859–861 1.000 68.4
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG CGTGCGGTGTAATTCCATTG 859–861 1.000 66.5
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 858–860 1.000 66.5
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT TGGGTTGCTAACTCAATGGT 800–802 1.000 62.0
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA CGTGCGGTGTAATTCCATTG 859–861 1.000 61.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 690 1.000 66.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 691 1.000 65.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 688 1.000 65.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 687 1.000 65.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 689 1.000 64.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2107–2131 1.000 43.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 2120–2144 1.000 42.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 2121–2145 1.000 42.9
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CCATGGCATTACTCTACCACC 2110–2134 1.000 42.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2109–2133 1.000 42.6
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1072 1.000 48.2
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1104 1.000 46.8
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1073 1.000 45.2
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1072 1.000 45.2
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1073 1.000 44.1
psbM-petN_p1 psbM-petN TGGAAGTCAATATTCTCGCA TAGTAAGTCTCGCTTGGGCT 941–960 1.000 50.8
psbM-petN_p2 psbM-petN TGGAAGTCAATATTCTCGCA GTAGTATGGGGGAGGAGTGG 885–904 1.000 49.8
psbM-petN_p3 psbM-petN TGGAAGTCAATATTCTCGCA TAGTATGGGGGAGGAGTGGA 884–903 1.000 49.0
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTTATTCT TAGTAAGTCTCGCTTGGGCT 916–935 1.000 48.9
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTTATTCT GTAGTATGGGGGAGGAGTGG 860–879 1.000 47.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Sinobambusa intermedia OQ220334.1 139797 View on NCBI ↗
Sinobambusa rubroligula NC_082098.1 139839 View on NCBI ↗
Sinobambusa striata OQ130031.1 139749 View on NCBI ↗
Sinobambusa tootsik PQ472937.1 139709 View on NCBI ↗
Sinobambusa tootsik f. albostriata PQ472936.1 139678 View on NCBI ↗
Sinobambusa tootsik var. dentata PP681656.1 139678 View on NCBI ↗
Sinobambusa tootsik var. laeta OQ236108.1 139709 View on NCBI ↗