Markers + reference

Arrhenatherum

2 species · Poaceae · Poales

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Species 2
Genome length 134–136 kb
Candidate markers 261
Primer pairs 60

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 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 40.0 yes View details
rpoB LSC 3231 0.0003 1.00 55.4 yes View details
atpA LSC 1524 0.0007 1.00 59.1 yes View details
ndhH IRb 207 0.0531 1.00 81.6 yes View details
ndhF-rpl32 SSC 815 0.0013 0.96 58.2 no View details
rpl32-trnL-UAG SSC 633 0.0000 0.99 59.5 no View details
ndhH SSC 1182 0.0000 1.00 40.0 no View details
trnN-GUU-rps15 IRb 1558 0.0000 1.00 58.9 yes View details
rps15-trnN-GUU IRa 1558 0.0000 1.00 58.9 yes View details
ndhC-trnV-UAC LSC 866 0.0000 0.99 58.4 yes View details
rpl23-psbA LSC 167 0.0000 0.56 47.0 no View details
matK-trnK-UUU LSC 664 0.0000 1.00 40.0 yes View details
rps16 LSC 1116 0.0000 1.00 40.0 yes View details
rps16-trnQ-UUG LSC 614 0.0000 1.00 40.0 yes View details
trnS-GCU-psbD LSC 963 0.0000 1.00 40.0 yes View details
psbD LSC 1062 0.0000 1.00 40.0 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGGGTATTTCTGGCTTTTCT AATACGTGTGCTTGGGAGTC 1167 1.000 51.3
psbA_p2 psbA TGGGTATTTCTGGCTTTTCTT AATACGTGTGCTTGGGAGTC 1167 1.000 50.2
psbA_p3 psbA TTGGGTATTTCTGGCTTTTCT AATACGTGTGCTTGGGAGTC 1168 1.000 50.2
psbA_p4 psbA TGGGTATTTCTGGCTTTTCTTTC AATACGTGTGCTTGGGAGTC 1167 1.000 49.5
psbA_p5 psbA TGGGTATTTCTGGCTTTTCTTT AATACGTGTGCTTGGGAGTC 1167 1.000 48.4
matK-trnK-UUU_p1 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT AGAAGCGCCCAGTGTAATTC 844 1.000 61.7
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAAGAGAAGTGGGTAGA AGAAGCGCCCAGTGTAATTC 843 1.000 60.9
matK-trnK-UUU_p3 matK-trnK-UUU TTCCTGAAAGAGAAGTGGGT AATGTTTTGACAGAAGCGCC 855 1.000 60.4
matK-trnK-UUU_p4 matK-trnK-UUU CCTGAAAGAGAAGTGGGTAGAC AGAAGCGCCCAGTGTAATTC 842 1.000 60.4
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAAGAGAAGTGGGTAGA AATGTTTTGACAGAAGCGCC 854 1.000 59.6
rps16_p1 rps16 ATGTTGGATTGGCACGACAT ACCACTTTGCAATGAAAAGAGG 1259 1.000 60.1
rps16_p2 rps16 GCTTATGTTGGATTGGCACG ACCACTTTGCAATGAAAAGAGG 1263 1.000 59.8
rps16_p3 rps16 ATGTTGGATTGGCACGACAT CCACTTTGCAATGAAAAGAGGA 1258 1.000 58.0
rps16_p4 rps16 GCTTATGTTGGATTGGCACG CCACTTTGCAATGAAAAGAGGA 1262 1.000 57.7
rps16_p5 rps16 AGGGGCTTATGTTGGATTGG ACCACTTTGCAATGAAAAGAGG 1267 1.000 57.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 687 1.000 78.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 698 1.000 77.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGTGTCGCATAAAACCCGAA 756 1.000 77.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 691 1.000 77.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC AGTGTCGCATAAAACCCGAA 767 1.000 77.0
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1108 1.000 78.3
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TCCTACAAAAACGAAGCGGT 1099 1.000 77.7
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CCCTTCGTAACCAGTCATCC 1079 1.000 77.2
trnS-GCU-psbD_p4 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC GCCGGACCATCCTACAAAAA 1159 1.000 76.8
trnS-GCU-psbD_p5 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC TCCTACAAAAACGAAGCGGT 1150 1.000 76.2
psbD_p1 psbD GACATGAGGTGCTCGGAAAT AGTGGTTTCTTGGTCACGAC 1151 1.000 79.4
psbD_p2 psbD GACATGAGGTGCTCGGAAAT CAGTGGTTTCTTGGTCACGA 1152 1.000 79.3
psbD_p3 psbD GACATGAGGTGCTCGGAAAT TCCAAGTAGCTTACCGGACA 1211 1.000 79.2
psbD_p4 psbD TTGGAAGTGACATGAGGTGC AGTGGTTTCTTGGTCACGAC 1159 1.000 78.8
psbD_p5 psbD TTGGAAGTGACATGAGGTGC CAGTGGTTTCTTGGTCACGA 1160 1.000 78.8

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
Arrhenatherum elatius NC_042673.1 134242 View on NCBI ↗
Arrhenatherum elatius subsp. elatius PP316520.1 136375 View on NCBI ↗