Markers + reference

Briza

2 species · Poaceae · Poales

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Species 2
Genome length 135–137 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 820 0.0420 0.84 73.5 yes View details
trnS-GCU-psbD LSC 910 0.0352 1.00 71.8 yes View details
trnT-UGU-ADO75_gt016 LSC 798 0.0310 0.89 72.4 yes View details
trnF-GAA-ndhJ LSC 586 0.0393 1.00 70.7 yes View details
ndhC-trnV-UAC LSC 910 0.0382 0.75 65.6 yes View details
petA-psbJ LSC 797 0.0354 0.99 66.4 yes View details
psbE-petL LSC 1156 0.0247 0.42 55.1 yes View details
ndhF SSC 2220 0.0189 1.00 53.5 yes View details
ndhF-rpl32 SSC 900 0.0399 0.98 69.8 yes View details
rpl32-trnL-UAG SSC 647 0.0376 0.95 76.8 yes View details
rps19-psbA IRa 643 0.0787 0.20 62.0 no View details
psbI-trnS-GCU LSC 109 0.0550 1.00 73.9 yes View details
ADO75_gt016-trnF-GAA LSC 345 0.0437 0.99 73.9 yes View details
petG-trnW-CCA LSC 122 0.0902 1.00 72.8 yes View details
ndhH-ndhF SSC 33 0.0909 1.00 71.6 yes View details
ycf3-trnS-GGA LSC 611 0.0313 0.99 71.1 yes View details
rpl22-rps19 IRb 60 0.0500 1.00 70.1 yes View details
trnD-GUC-psbM LSC 709 0.0275 0.97 70.0 yes View details
trnfM-CAU-trnG-UCC LSC 106 0.0294 0.96 69.9 yes View details
petN-trnC-GCA LSC 913 0.0303 0.97 69.8 yes View details
trnG-UCC-trnT-GGU LSC 1185 0.0272 0.93 69.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 796–893 1.000 85.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 807–904 1.000 84.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 800–897 1.000 83.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 811–908 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 802–899 1.000 82.2
psbI-trnS-GCU_p1 psbI-trnS-GCU TCTAATGACCCAGGACGGAA TAAAGCGGCGGATTGCTAAT 216–228 1.000 79.9
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCTAATGACCCAGGACGGA TAAAGCGGCGGATTGCTAAT 217–229 1.000 78.1
psbI-trnS-GCU_p3 psbI-trnS-GCU TCTAATGACCCAGGACGGAA ATGGCTGAGTGGACTAAAGC 230–242 1.000 76.8
psbI-trnS-GCU_p4 psbI-trnS-GCU TCTAATGACCCAGGACGGAA GAGAGATGGCTGAGTGGACT 235–247 1.000 75.9
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGACCCAGGACGGA ATGGCTGAGTGGACTAAAGC 231–243 1.000 75.0
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1042–1106 1.000 80.3
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CCCTTCGTAACCAGTCATCC 1026–1090 1.000 79.8
trnS-GCU-psbD_p3 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC ACAAAAACGAAACGGTCCCT 1093–1157 1.000 78.6
trnS-GCU-psbD_p4 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC CCCTTCGTAACCAGTCATCC 1077–1141 1.000 78.1
trnS-GCU-psbD_p5 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1034–1098 1.000 77.7
trnfM-CAU-trnG-UCC_p1 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG AGCCTTCCAAGCTAACGATG 197–198 1.000 80.7
trnfM-CAU-trnG-UCC_p2 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCTAGCCTTCCAAGCTAACG 200–201 1.000 80.5
trnfM-CAU-trnG-UCC_p3 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG AGCCTTCCAAGCTAACGATG 182–183 1.000 80.5
trnfM-CAU-trnG-UCC_p4 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG CCTAGCCTTCCAAGCTAACG 185–186 1.000 80.3
trnfM-CAU-trnG-UCC_p5 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCAACGTCGACTATAACCCC 218–219 1.000 79.0
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1246–1275 1.000 46.6
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1242–1271 1.000 45.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1243–1272 1.000 45.9
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 1249–1278 1.000 45.9
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1248–1277 1.000 45.9
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 807–820 1.000 62.0
trnD-GUC-psbM_p2 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 808–821 1.000 57.8
trnD-GUC-psbM_p3 trnD-GUC-psbM CGCGGGGATTGTAGTTCAA AGAATGAACAGTGCAGTAGC 821–834 1.000 56.6
trnD-GUC-psbM_p4 trnD-GUC-psbM GGTATGCCATACATCCCGC AGAATGAACAGTGCAGTAGC 837–850 1.000 56.5
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 806–819 1.000 56.0

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
Briza maxima NC_027471.1 136823 View on NCBI ↗
Briza media NC_067043.1 135218 View on NCBI ↗