Markers + reference

Bromus

5 species · Poaceae · Poales

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Species 5
Genome length 136–137 kb
Candidate markers 272
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 743 0.0171 1.00 61.3 yes View details
trnY-GUA-trnD-GUC LSC 349 0.0252 1.00 54.7 yes View details
petN-trnC-GCA LSC 931 0.0158 1.00 67.3 yes View details
trnC-GCA-rpoB LSC 1165 0.0159 1.00 64.5 yes View details
ndhC-trnV-UAC LSC 919 0.0201 0.98 65.4 yes View details
rbcL-psaI LSC 1713 0.0162 0.99 58.2 yes View details
ndhH IRb 336 0.0779 0.84 73.7 yes View details
ndhF SSC 2220 0.0081 1.00 48.2 yes View details
ndhF-rpl32 SSC 874 0.0223 0.91 77.3 yes View details
ndhH SSC 1182 0.0102 1.00 56.5 no View details
rps19-psbA LSC 116 0.0448 0.98 76.1 no View details
rpl32-trnL-UAG SSC 740 0.0172 0.99 72.9 yes View details
rpl22-rps19 LSC 79 0.0329 1.00 71.9 yes View details
trnS-GCU-psbD LSC 911 0.0114 0.98 66.1 yes View details
ndhH-ndhF SSC 15 0.0867 1.00 65.5 yes View details
trnK-UUU-rps16 LSC 581 0.0120 0.98 64.9 yes View details
trnP-UGG-psaJ LSC 398 0.0100 0.98 64.0 yes View details
trnG-UCC-trnT-GGU LSC 1220 0.0126 1.00 63.5 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GCTCAACCGACAAGAACTGT 686–705 1.000 76.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GTGCTCAACCGACAAGAACT 688–707 1.000 76.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TGCTCAACCGACAAGAACTG 687–706 1.000 76.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GCTCAACCGACAAGAACTGT 684–703 1.000 75.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GTGCTCAACCGACAAGAACT 686–705 1.000 75.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 816–846 1.000 80.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 827–857 1.000 80.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 820–850 1.000 79.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 831–861 1.000 79.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 822–852 1.000 77.8
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAGCAATAGGCCAGACCATC 1051–1077 1.000 82.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1029–1055 1.000 81.2
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CCCTTCGTAACCAGTCATCC 1013–1039 1.000 80.7
trnS-GCU-psbD_p4 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC GAGCAATAGGCCAGACCATC 1102–1128 1.000 80.5
trnS-GCU-psbD_p5 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA AGGCCAGACCATCCTACAAA 1044–1070 1.000 80.5
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTGAGTTAAAAGGGCT 1217–1300 1.000 46.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1254–1337 1.000 46.5
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACCACTGAGTTAAAAGGGCT 1219–1302 1.000 45.8
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1250–1333 1.000 45.7
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1251–1334 1.000 45.7
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 472–483 1.000 78.4
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 439–450 1.000 76.1
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 438–449 1.000 75.9
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 471–482 1.000 74.2
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC GATGCCCGAGTGGTTAATGG CGGTGCTCTGACCAATTGAA 457–468 1.000 73.3
petN-trnC-GCA_p1 petN-trnC-GCA AGTCCACTCCTTCCCCATAC AGTTCAAATCTGGGTGCCG 913–1044 1.000 76.8
petN-trnC-GCA_p2 petN-trnC-GCA GTCCACTCCTTCCCCATACT AGTTCAAATCTGGGTGCCG 912–1043 1.000 76.8
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 854–985 1.000 76.7
petN-trnC-GCA_p4 petN-trnC-GCA GTCCACTCCTTCCCCATACT CCAGTTCAAATCTGGGTGCC 914–1045 1.000 76.4
petN-trnC-GCA_p5 petN-trnC-GCA AGTCCACTCCTTCCCCATAC CCAGTTCAAATCTGGGTGCC 915–1046 1.000 76.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Bromus benekenii PP328785.1 137297 View on NCBI ↗
Bromus hordeaceus subsp. hordeaceus PP328781.1 137163 View on NCBI ↗
Bromus inermis subsp. inermis PP328782.1 137153 View on NCBI ↗
Bromus sterilis PP328786.1 136054 View on NCBI ↗
Bromus tectorum PP328787.1 136872 View on NCBI ↗