Markers + reference

Bonia

2 species · Poaceae · Poales

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Species 2
Genome length 138–139 kb
Candidate markers 257
Primer pairs 80

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 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 29.7 yes View details
trnG-UCC-trnT-GGU LSC 2995 0.0050 1.00 56.8 yes View details
trnT-GGU-trnE-UUC LSC 534 0.0075 1.00 61.7 yes View details
rps14 LSC 312 0.0000 1.00 19.8 yes View details
petA-psbJ LSC 983 0.0061 1.00 62.3 yes View details
psbH LSC 222 0.0045 1.00 55.1 yes View details
rpl32-trnL-UAG SSC 719 0.0097 1.00 56.2 yes View details
trnL-CAA-trnI-CAU IRa 2506 0.0016 0.99 58.3 yes View details
psbT-psbN LSC 48 0.1042 1.00 87.5 yes View details
rps14-psaB LSC 101 0.0594 1.00 82.4 yes View details
rps19-psbA LSC 230 0.0336 0.52 63.8 no View details
trnH-GUG-rpl2 IRb 55 0.0182 1.00 63.0 yes View details
rpl2-trnH-GUG IRa 55 0.0182 1.00 63.0 yes View details
rpl20-rps12 LSC 696 0.0043 1.00 61.7 yes View details
psbM-petN LSC 750 0.0014 0.98 61.3 yes View details
ndhF-rpl32 SSC 901 0.0044 1.00 61.3 yes View details
rps18 LSC 534 0.0000 0.96 61.2 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
psbA_p1 psbA TCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1159 1.000 68.5
psbA_p2 psbA TTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1160 1.000 68.5
psbA_p3 psbA TCTGGCTTTCCTTCCTTCAAA AATACGTGTGCTTGGGAGTC 1159 1.000 66.5
psbA_p4 psbA TTCTGGCTTTCCTTCCTTCAA AATACGTGTGCTTGGGAGTC 1160 1.000 66.5
psbA_p5 psbA TTTCTGGCTTTCCTTCCTTCA AATACGTGTGCTTGGGAGTC 1161 1.000 66.5
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU GAAAACCCATAGCCAGGAGG GGACGGATTTGTTGAAGCGA 242 1.000 74.4
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU CCCATAGCCAGGAGGAGTTA GGACGGATTTGTTGAAGCGA 237 1.000 74.1
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU TTTTTGTTGGGCAGGCAGTA GGACGGATTTGTTGAAGCGA 193 1.000 73.6
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU GAAAACCCATAGCCAGGAGG TTGGACGGATTTGTTGAAGC 244 1.000 72.5
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU AAAACCCATAGCCAGGAGGA GGACGGATTTGTTGAAGCGA 241 1.000 72.3
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 655 1.000 67.6
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 634 1.000 67.5
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 618 1.000 67.4
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 597 1.000 67.3
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 623 1.000 66.7
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 898–912 1.000 68.9
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTAGTATGGGGGAGGAGTGG 842–856 1.000 67.9
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTATGGGGGAGGAGTGGA 841–855 1.000 67.2
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTC TAGTAAGTCTCGCTTGGGCT 898–912 1.000 64.7
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT AGTAGTATGGGGGAGGAGTG 843–857 1.000 63.9
rps14_p1 rps14 TAGCAAGACATTCACCGAGC GTATGGGCGTGGATGTTCTT 1358–1413 1.000 80.0
rps14_p2 rps14 TAGCAAGACATTCACCGAGC TTTCCTGGCGTGGATATTGG 1297–1352 1.000 79.9
rps14_p3 rps14 TAGCAAGACATTCACCGAGC TAGTTTTCCTTGTGACGGCC 1626–1681 1.000 79.4
rps14_p4 rps14 AGCCTTGTGAGCTACCAAAC GTATGGGCGTGGATGTTCTT 880–936 1.000 79.4
rps14_p5 rps14 AGCCTTGTGAGCTACCAAAC TTTCCTGGCGTGGATATTGG 819–875 1.000 79.3
rps14-psaB_p1 rps14-psaB CTCAAGGGGGAAACTTTGCT GCAGCTTTCTTGATTGCCTC 259–315 1.000 79.5
rps14-psaB_p2 rps14-psaB CTCAAGGGGGAAACTTTGCT GCTCTTTCCATTGTGCAAGC 328–384 1.000 79.0
rps14-psaB_p3 rps14-psaB CTCAAGGGGGAAACTTTGCT TGGCTCTTTCCATTGTGCAA 330–386 1.000 78.9
rps14-psaB_p4 rps14-psaB CTCAAGGGGGAAACTTTGCT TGCAGCTTTCTTGATTGCCT 260–316 1.000 78.7
rps14-psaB_p5 rps14-psaB CTCAAGGGGGAAACTTTGCT GGCTCTTTCCATTGTGCAAG 329–385 1.000 78.5

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
Bonia levigata NC_085343.1 138382 View on NCBI ↗
Bonia saxatilis NC_050756.1 139007 View on NCBI ↗