Markers + reference

Phyllostachys

23 species · Poaceae · Poales

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Species 23
Genome length 140–140 kb
Candidate markers 265
Primer pairs 80

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
psbM-petN LSC 767 0.0022 0.99 46.7 yes View details
rpoC1 LSC 2049 0.0006 1.00 39.3 yes View details
atpI-atpH LSC 815 0.0000 1.00 27.0 yes View details
atpA LSC 1524 0.0003 1.00 40.2 yes View details
ycf3 LSC 2000 0.0007 1.00 41.1 yes View details
rbcL-psaI LSC 1289 0.0032 1.00 41.8 yes View details
rpl32-trnL-UAG SSC 702 0.0035 1.00 42.8 yes View details
matK-trnK-UUU LSC 695 0.0006 1.00 42.3 yes View details
psaA-ycf3 LSC 632 0.0000 0.99 42.2 yes View details
rps15-ndhF IRb 450 0.0000 1.00 42.1 yes View details
rps19-psbA LSC 129 0.0000 1.00 41.4 no View details
psbC LSC 1422 0.0003 1.00 41.2 yes View details
trnT-UGU-trnL-UAA LSC 820 0.0005 1.00 40.8 yes View details
ndhK LSC 741 0.0007 1.00 40.5 yes View details
petB LSC 1466 0.0002 1.00 40.5 yes View details
trnS-GCU-psbD LSC 982 0.0003 1.00 40.4 yes View details
psbZ-trnG-UCC LSC 943 0.0005 1.00 40.4 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 861–865 1.000 68.8
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG CGTGCGGTGTAATTCCATTG 861–865 1.000 67.0
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 860–864 1.000 67.0
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT TGGGTTGCTAACTCAATGGT 802–806 1.000 62.5
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA CGTGCGGTGTAATTCCATTG 861–865 1.000 62.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1127–1128 1.000 78.5
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1114–1115 1.000 77.9
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1113–1114 1.000 75.5
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1106–1107 1.000 75.3
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1100–1101 1.000 74.9
psbC_p1 psbC TTCGTTTCCCAGGAAATCCG TGGCTCGGCTAGATGGAATA 1608 1.000 78.6
psbC_p2 psbC GCAGCGGAAGATCCTGAATT TGGCTCGGCTAGATGGAATA 1587 1.000 77.5
psbC_p3 psbC TTCGTTTCCCAGGAAATCCG AACCGAGCCAGAACAGAAAA 1589 1.000 75.9
psbC_p4 psbC TTCGTTTCCCAGGAAATCCG ACCGAGCCAGAACAGAAAAA 1588 1.000 75.9
psbC_p5 psbC TTCGTTTCCCAGGAAATCCG GGAATAACCGAGCCAGAACA 1594 1.000 75.5
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG AGCCTTCCAAGCTAACGATG 1097 1.000 78.2
psbZ-trnG-UCC_p2 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG CCTAGCCTTCCAAGCTAACG 1100 1.000 78.0
psbZ-trnG-UCC_p3 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC AGCCTTCCAAGCTAACGATG 1095 1.000 77.8
psbZ-trnG-UCC_p4 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTC CCTAGCCTTCCAAGCTAACG 1098 1.000 77.6
psbZ-trnG-UCC_p5 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG CCAACGTCGACTATAACCCC 1118 1.000 76.7
psbM-petN_p1 psbM-petN TGGAAGTCAATATTCTCGCA TAGTAAGTCTCGCTTGGGCT 939–954 1.000 52.6
psbM-petN_p2 psbM-petN TGGAAGTCAATATTCTCGCA GTAGTATGGGGGAGGAGTGG 883–898 1.000 51.7
psbM-petN_p3 psbM-petN TGGAAGTCAATATTCTCGCA TAGTATGGGGGAGGAGTGGA 882–897 1.000 50.9
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTTATTCT TAGTAAGTCTCGCTTGGGCT 914–929 1.000 50.7
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTTATTCT GTAGTATGGGGGAGGAGTGG 858–873 1.000 49.8
rpoC1_p1 rpoC1 AGGGAGGAAGTTTGATCGGA GCGCGGCAAAAATGATGATA 2173 1.000 78.8
rpoC1_p2 rpoC1 AGGGAGGAAGTTTGATCGGA ACTAGCGAAATCGGAATGCC 2154 1.000 76.4
rpoC1_p3 rpoC1 AGGGAGGAAGTTTGATCGGA GGCATCGCCGAATCTAACTT 2120 1.000 76.4
rpoC1_p4 rpoC1 AGGGAGGAAGTTTGATCGGA ATCTCAATCTGGATTCGCGC 2189 1.000 75.8
rpoC1_p5 rpoC1 GGGAGGAAGTTTGATCGGAA GCGCGGCAAAAATGATGATA 2172 1.000 72.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Phyllostachys angusta NC_053647.1 139678 View on NCBI ↗
Phyllostachys aurea KU569973.1 139695 View on NCBI ↗
Phyllostachys aureosulcata f. spectabilis PQ472922.1 139701 View on NCBI ↗
Phyllostachys edulis NC_015817.1 139679 View on NCBI ↗
Phyllostachys edulis f. bicolor OM084949.1 139678 View on NCBI ↗
Phyllostachys edulis f. exaurita PP453779.1 139668 View on NCBI ↗
Phyllostachys edulis f. gracilis PP453784.1 139678 View on NCBI ↗
Phyllostachys edulis f. holochrysa PP453781.1 139678 View on NCBI ↗
Phyllostachys edulis f. luteosulcata OR597504.1 139678 View on NCBI ↗
Phyllostachys edulis f. nabeshimana PP453782.1 139678 View on NCBI ↗
Phyllostachys glauca NC_051535.1 139689 View on NCBI ↗
Phyllostachys heteroclada NC_064526.1 139701 View on NCBI ↗
Phyllostachys heteroclada f. solida MW075109.1 139678 View on NCBI ↗
Phyllostachys incarnata NC_067630.1 139689 View on NCBI ↗
Phyllostachys lithophila NC_062169.1 139664 View on NCBI ↗
Phyllostachys makinoi NC_062168.1 139657 View on NCBI ↗
Phyllostachys nigra PQ472924.1 139708 View on NCBI ↗
Phyllostachys nigra var. henonis NC_015826.1 139839 View on NCBI ↗
Phyllostachys praecox NC_067631.1 139715 View on NCBI ↗
Phyllostachys reticulata PP545476.1 139689 View on NCBI ↗
Phyllostachys sulphurea NC_024669.1 139731 View on NCBI ↗
Phyllostachys violascens NC_068835.1 139850 View on NCBI ↗
Phyllostachys vivax f. aureocaulis PQ472927.1 139715 View on NCBI ↗