Markers + reference

Avena

27 species · Poaceae · Poales

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Species 27
Genome length 135–136 kb
Candidate markers 277
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl23 LSC 279 0.0050 1.00 26.5 yes View details
petA-psbJ LSC 693 0.0056 1.00 50.3 yes View details
petL-petG LSC 176 0.0052 1.00 33.6 yes View details
rpl16 LSC 1459 0.0037 1.00 33.5 yes View details
rpl23 IRb 282 0.0003 1.00 23.5 no View details
ndhF-rpl32 SSC 848 0.0056 1.00 42.5 yes View details
rpl32-trnL-UAG SSC 631 0.0106 1.00 44.2 yes View details
ccsA SSC 960 0.0025 1.00 29.8 yes View details
rpl23 IRa 282 0.0003 1.00 23.5 no View details
trnG-UCC-trnI LSC 682 0.0043 1.00 53.1 yes View details
trnD-GUC-psbM LSC 700 0.0043 1.00 50.1 yes View details
rps16-trnQ-UUG LSC 790 0.0042 1.00 49.3 yes View details
psaA-ycf3 LSC 643 0.0037 1.00 48.2 yes View details
trnT-UGU-trnL-UAA LSC 814 0.0038 1.00 47.9 yes View details
psbE-petL LSC 1272 0.0023 1.00 47.5 yes View details
rps12a-trnT-GGU LSC 378 0.0046 1.00 46.5 yes View details
trnR-UCU-trnfM LSC 114 0.0121 1.00 46.4 yes View details
psbK-psbI LSC 408 0.0056 1.00 46.3 yes View details
trnY-GUA-trnD-GUC LSC 315 0.0053 1.00 44.8 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 85 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 852–890 1.000 81.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 863–901 1.000 80.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGTGTCGCATAAAACCCGAA 921–959 1.000 80.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 856–894 1.000 80.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC AGTGTCGCATAAAACCCGAA 932–970 1.000 79.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GATTCCGTCCTGGGTCATTG 521–533 1.000 80.4
psbK-psbI_p2 psbK-psbI CGTGGATGTTATGCCTGTCA GATTCCGTCCTGGGTCATTG 570–582 1.000 80.3
psbK-psbI_p3 psbK-psbI CGTGGATGTTATGCCTGTCA GAATTTTTACTCCTCGCGCC 593–605 1.000 79.2
psbK-psbI_p4 psbK-psbI CGTGGATGTTATGCCTGTCA GGAATTTTTACTCCTCGCGC 594–606 1.000 79.2
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GAATTTTTACTCCTCGCGCC 544–556 1.000 79.2
trnG-UCC-trnI_p1 trnG-UCC-trnI ACGAATCACACTTTTACCACT GCGGATTCTGGAACCCTAAG 832–840 0.926 51.0
trnG-UCC-trnI_p2 trnG-UCC-trnI AGAACGAATCACACTTTTACCAC GCGGATTCTGGAACCCTAAG 835–843 0.926 49.9
trnG-UCC-trnI_p3 trnG-UCC-trnI GAACGAATCACACTTTTACCACT GCGGATTCTGGAACCCTAAG 834–842 0.926 49.9
trnG-UCC-trnI_p4 trnG-UCC-trnI AACGAATCACACTTTTACCACT GCGGATTCTGGAACCCTAAG 833–841 0.926 49.1
trnG-UCC-trnI_p5 trnG-UCC-trnI TACCACTAAACTATACCCGC GCGGATTCTGGAACCCTAAG 818–826 0.926 47.2
rps12a-trnT-GGU_p1 rps12a-trnT-GGU ACCAAATGTTCCTTCCACGA CGTCTTAGCACGGCATTACT 543 0.926 72.5
rps12a-trnT-GGU_p2 rps12a-trnT-GGU ACCAAATGTTCCTTCCACGA CTTACGTCTTAGCACGGCAT 547 0.926 72.5
rps12a-trnT-GGU_p3 rps12a-trnT-GGU ACCAAATGTTCCTTCCACGA ACGTCTTAGCACGGCATTAC 544 0.926 70.3
rps12a-trnT-GGU_p4 rps12a-trnT-GGU ACCAAATGTTCCTTCCACGA TTACGTCTTAGCACGGCATT 546 0.926 70.2
rps12a-trnT-GGU_p5 rps12a-trnT-GGU ACCAAATGTTCCTTCCACGAA CGTCTTAGCACGGCATTACT 543 0.926 69.3
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 434–439 1.000 78.7
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 401–406 1.000 76.5
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 400–405 1.000 76.3
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 433–438 1.000 74.6
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 402–407 1.000 73.1
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 611–827 1.000 63.9
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGGAACTAGAATGAACAGTGCA 618–834 1.000 60.8
trnD-GUC-psbM_p3 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 612–828 1.000 59.8
trnD-GUC-psbM_p4 trnD-GUC-psbM CGCGGGGATTGTAGTTCAA AGAATGAACAGTGCAGTAGC 625–841 1.000 58.6
trnD-GUC-psbM_p5 trnD-GUC-psbM GGTATGCCATACATCCCGC AGAATGAACAGTGCAGTAGC 641–857 1.000 58.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (27)

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

Species Accession Length (bp) Link
Avena abyssinica NC_044158.1 135942 View on NCBI ↗
Avena agadiriana NC_044159.1 135945 View on NCBI ↗
Avena atlantica NC_044163.1 136006 View on NCBI ↗
Avena barbata NC_044173.1 135946 View on NCBI ↗
Avena brevis NC_044172.1 135939 View on NCBI ↗
Avena canariensis NC_044161.1 135955 View on NCBI ↗
Avena clauda NC_044167.1 135557 View on NCBI ↗
Avena damascena NC_044166.1 135925 View on NCBI ↗
Avena eriantha NC_044157.1 135560 View on NCBI ↗
Avena fatua NC_044170.1 135889 View on NCBI ↗
Avena hirtula NC_050395.1 135937 View on NCBI ↗
Avena hispanica NC_044164.1 135935 View on NCBI ↗
Avena hybrida NC_044148.1 135900 View on NCBI ↗
Avena insularis MG674209.1 135967 View on NCBI ↗
Avena longiglumis OP805352.1 135378 View on NCBI ↗
Avena lusitanica NC_044149.1 135879 View on NCBI ↗
Avena maroccana NC_044162.1 135887 View on NCBI ↗
Avena murphyi NC_044174.1 135892 View on NCBI ↗
Avena nuda NC_044147.1 135934 View on NCBI ↗
Avena occidentalis NC_044175.1 135893 View on NCBI ↗
Avena sativa NC_027468.1 135890 View on NCBI ↗
Avena sterilis NC_031650.1 135887 View on NCBI ↗
Avena sterilis subsp. ludoviciana PP328777.1 135899 View on NCBI ↗
Avena strigosa NC_044171.1 135938 View on NCBI ↗
Avena vaviloviana NC_044168.1 135946 View on NCBI ↗
Avena ventricosa NC_044165.1 135681 View on NCBI ↗
Avena wiestii NC_044160.1 135944 View on NCBI ↗