Markers + reference

Eremopyrum

2 species · Poaceae · Poales

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Species 2
Genome length 135–136 kb
Candidate markers 265
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 516 0.0117 0.99 63.4 yes View details
psbK-psbI LSC 406 0.0148 1.00 63.2 yes View details
trnG-UCC-trnM-CAU LSC 1130 0.0098 0.99 64.9 yes View details
trnL-UAA-trnF-GAA LSC 351 0.0202 0.99 61.1 yes View details
psaJ-rpl33 LSC 440 0.0289 0.86 73.4 yes View details
ndhF-rpl32 SSC 909 0.0119 0.93 66.4 yes View details
rpl32-trnL-UAG SSC 699 0.0078 0.92 54.6 yes View details
rps3-rpl22 LSC 60 0.0345 0.97 75.4 yes View details
psbL-psbF LSC 22 0.0455 1.00 74.4 yes View details
rpoB-rpoC1 LSC 37 0.0714 0.38 70.6 yes View details
rps16-trnQ-UUG LSC 750 0.0107 0.99 65.4 yes View details
psaC-ndhE SSC 470 0.0088 0.96 64.6 yes View details
trnT-UGU-trnL-UAA LSC 607 0.0083 1.00 63.7 yes View details
ndhC-trnV-UAC LSC 905 0.0056 0.98 63.6 yes View details
psbM-petN LSC 549 0.0041 0.89 63.2 yes View details
trnF-GAA-ndhJ LSC 597 0.0053 0.95 63.2 yes View details
clpP-psbB LSC 510 0.0021 0.95 62.8 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 CAACCAAGTCAGCCCAAAGA AATGTTTTGACAGAAGCGCG 2724–2750 1.000 78.7
trnK-UUU_p2 trnK-UUU TCAACCAAGTCAGCCCAAAG AATGTTTTGACAGAAGCGCG 2725–2751 1.000 78.7
trnK-UUU_p3 trnK-UUU AATGTCAACCAAGTCAGCCC AATGTTTTGACAGAAGCGCG 2729–2755 1.000 78.1
trnK-UUU_p4 trnK-UUU GTCAACCAAGTCAGCCCAAA AATGTTTTGACAGAAGCGCG 2726–2752 1.000 76.3
trnK-UUU_p5 trnK-UUU ACCAAGTCAGCCCAAAGATT AATGTTTTGACAGAAGCGCG 2722–2748 1.000 75.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GCTCAACCGACAAGAACTGT 647–650 1.000 73.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GTGCTCAACCGACAAGAACT 649–652 1.000 73.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TGCTCAACCGACAAGAACTG 648–651 1.000 73.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GCTCAACCGACAAGAACTGT 645–648 1.000 72.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GTGCTCAACCGACAAGAACT 647–650 1.000 72.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 820–824 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 831–835 1.000 78.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGTGTCGCATAAAACCCGAA 889–893 1.000 78.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 824–828 1.000 78.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC AGTGTCGCATAAAACCCGAA 900–904 1.000 78.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCGCGTCCAG 550 1.000 79.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCCGTCCTGGGTCATTAGA 528 1.000 78.5
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTACTCCTCGCGTCCAG 547 1.000 77.8
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTTTTACTCCTCGCGTCCAG 548 1.000 77.8
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTTTTACTCCTCGCGTCCAG 549 1.000 77.8
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1213–1214 1.000 41.9
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGACTTACGTCTTAGCACGAG 1273–1274 1.000 41.1
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1209–1210 1.000 41.1
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1210–1211 1.000 41.1
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1215–1216 1.000 41.1
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT AGTATGGGGAAGGAGTGGAC 587–653 1.000 72.0
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTATGGGGAAGGAGTGGACT 586–652 1.000 72.0
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 645–711 1.000 71.8
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTCT TATGGGGAAGGAGTGGACTC 585–651 1.000 71.6
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT GGGGAAGGAGTGGACTCTAG 582–648 1.000 71.3

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
Eremopyrum orientale NC_059955.1 135680 View on NCBI ↗
Eremopyrum triticeum NC_059978.1 134974 View on NCBI ↗