Markers + reference

Shibataea

3 species · Poaceae · Poales

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Species 3
Genome length 140–140 kb
Candidate markers 266
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psaA LSC 2253 0.0003 1.00 44.9 yes View details
ycf3 LSC 1987 0.0003 1.00 45.5 yes View details
trnT-UGU-trnL-UAA LSC 823 0.0008 1.00 46.8 yes View details
rbcL LSC 1434 0.0000 1.00 34.5 yes View details
rbcL-psaI LSC 1249 0.0037 1.00 61.1 yes View details
ndhF SSC 2220 0.0003 1.00 44.9 yes View details
rps15-trnN-GUU IRa 1541 0.0004 1.00 46.4 yes View details
trnR-ACG-rrn5 IRa 258 0.0000 1.00 30.0 yes View details
matK-trnK-UUU LSC 696 0.0010 1.00 59.5 yes View details
psbE-petL LSC 1228 0.0011 1.00 59.4 yes View details
infA LSC 393 0.0000 0.95 58.4 yes View details
trnfM-CAU-trnT-GGU LSC 2769 0.0002 1.00 57.2 yes View details
ndhC-trnV-UAC LSC 774 0.0000 1.00 50.2 yes View details
psbM-petN LSC 759 0.0000 1.00 47.0 yes View details
rps3 LSC 720 0.0009 1.00 46.8 yes View details
petA LSC 963 0.0007 1.00 46.7 yes View details
rps16 LSC 1087 0.0006 1.00 46.6 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 TACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2759–2760 1.000 73.4
trnK-UUU_p2 trnK-UUU ACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2758–2759 1.000 73.4
trnK-UUU_p3 trnK-UUU ATACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2760–2761 1.000 69.4
trnK-UUU_p4 trnK-UUU TACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2759–2760 1.000 66.8
trnK-UUU_p5 trnK-UUU CAATGTCAACCAAGCCAGC CGTGCGGTGTAATTCCATTG 2756–2757 1.000 66.7
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 864–865 1.000 68.4
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG CGTGCGGTGTAATTCCATTG 864–865 1.000 66.5
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 863–864 1.000 66.5
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT TGGGTTGCTAACTCAATGGT 805–806 1.000 62.0
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA CGTGCGGTGTAATTCCATTG 864–865 1.000 61.7
rps16_p1 rps16 AGCACGACATAAATCCAGTCA GGGTCAATTCCCTATACCACT 1255 1.000 47.0
rps16_p2 rps16 AGCACGACATAAATCCAGTCA GGGTCAATTCCCTATACCACTT 1255 1.000 44.9
rps16_p3 rps16 AGCACGACATAAATCCAGTCA TCCCTATACCACTTTGCAATGA 1247 1.000 44.4
rps16_p4 rps16 ACGAGGGATACTAGTGATCCTC GGGTCAATTCCCTATACCACT 1188 1.000 43.7
rps16_p5 rps16 AGCACGACATAAATCCAGTCAA GGGTCAATTCCCTATACCACT 1255 1.000 43.4
trnfM-CAU-trnT-GGU_p1 trnfM-CAU-trnT-GGU CCTCAAGGTTATGAGCCTCG CCATGGCATTACTCTACCACC 2897–2917 1.000 69.6
trnfM-CAU-trnT-GGU_p2 trnfM-CAU-trnT-GGU CCTCGTGAGCTACCAAACTG CCATGGCATTACTCTACCACC 2882–2902 1.000 69.2
trnfM-CAU-trnT-GGU_p3 trnfM-CAU-trnT-GGU CCTCAAGGTTATGAGCCTCG GACTTACGTCTTACCATGGCA 2910–2930 1.000 68.9
trnfM-CAU-trnT-GGU_p4 trnfM-CAU-trnT-GGU CCTCAAGGTTATGAGCCTCG TGACTTACGTCTTACCATGGC 2911–2931 1.000 68.9
trnfM-CAU-trnT-GGU_p5 trnfM-CAU-trnT-GGU CCTCGTGAGCTACCAAACTG GACTTACGTCTTACCATGGCA 2895–2915 1.000 68.5
psbM-petN_p1 psbM-petN TGGAAGTCAATATTCTCGCA TAGTAAGTCTCGCTTGGGCT 941–946 1.000 51.1
psbM-petN_p2 psbM-petN TGGAAGTCAATATTCTCGCA GTAGTATGGGGGAGGAGTGG 885–890 1.000 50.0
psbM-petN_p3 psbM-petN TGGAAGTCAATATTCTCGCA TAGTATGGGGGAGGAGTGGA 884–889 1.000 49.3
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTTATTCT TAGTAAGTCTCGCTTGGGCT 916–921 1.000 49.2
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTTATTCT GTAGTATGGGGGAGGAGTGG 860–865 1.000 48.2
psaA_p1 psaA AGCTAAGCCTTGGCTAAACC TTGGCGGGTCTCTTTGTATG 2362 1.000 78.1
psaA_p2 psaA GCTAAGCCTTGGCTAAACCT TTGGCGGGTCTCTTTGTATG 2361 1.000 78.1
psaA_p3 psaA AGCTAAGCCTTGGCTAAACC GTTGGCGGGTCTCTTTGTAT 2363 1.000 78.1
psaA_p4 psaA GCTAAGCCTTGGCTAAACCT GTTGGCGGGTCTCTTTGTAT 2362 1.000 78.1
psaA_p5 psaA AATACGACGAGTAGTGGGGT TTGGCGGGTCTCTTTGTATG 2386 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Shibataea chiangshanensis NC_036826.1 139737 View on NCBI ↗
Shibataea chinensis PP681662.1 139746 View on NCBI ↗
Shibataea kumasaca KU523578.1 139717 View on NCBI ↗