Markers + reference

Aegilops

13 species · Poaceae · Poales

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Species 13
Genome length 113–137 kb
Candidate markers 247
Primer pairs 85

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 247 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNAK-rps16 LSC 569 0.0107 1.00 39.5 yes View details
psbK-psbI LSC 368 0.0185 1.00 57.4 yes View details
LK95_t006-psbD LSC 1038 0.0060 1.00 54.0 yes View details
psbE-petL LSC 1164 0.0060 1.00 55.9 yes View details
ndhF-rpl32 SSC 908 0.0060 1.00 40.8 yes View details
rpl32-LK95_t054 SSC 714 0.0071 1.00 38.4 yes View details
ccsA SSC 969 0.0014 1.00 29.2 yes View details
psbT-psbN LSC 48 0.0673 1.00 67.1 yes View details
ccsA-ndhD SSC 166 0.0406 1.00 64.9 yes View details
petG-LK95_t035 LSC 121 0.0420 1.00 63.9 yes View details
psaC-ndhE SSC 477 0.0046 1.00 54.7 yes View details
LK95_t030-LK95_t032 LSC 1628 0.0013 1.00 53.6 yes View details
infA-rps8 LSC 173 0.0080 1.00 52.4 yes View details
LK95_t012-LK95_t014 LSC 1965 0.0026 1.00 51.3 yes View details
rbcL-rpl23 LSC 311 0.0095 1.00 51.3 yes View details
psbM-petN LSC 632 0.0024 1.00 49.8 yes View details
LK95_t020-psbM LSC 815 0.0046 1.00 49.7 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
tRNAK-rps16_p1 tRNAK-rps16 TGAGGATCAGTCGTGGTCTT TCGAGCCGTATGAGGAGAAA 991–993 1.000 79.3
tRNAK-rps16_p2 tRNAK-rps16 TGAGGATCAGTCGTGGTCTT TTTCTCGAGCCGTATGAGGA 995–997 1.000 79.3
tRNAK-rps16_p3 tRNAK-rps16 ACGTCTAATTAGAGCGGGGA TCGAGCCGTATGAGGAGAAA 1172–1174 1.000 79.2
tRNAK-rps16_p4 tRNAK-rps16 ACGTCTAATTAGAGCGGGGA TTTCTCGAGCCGTATGAGGA 1176–1178 1.000 79.2
tRNAK-rps16_p5 tRNAK-rps16 TAGGAAGTTCAGCTCGTTGC TCGAGCCGTATGAGGAGAAA 1141–1143 1.000 79.1
psbK-psbI_p1 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACAAAAAGTTTGAGAGTAAGCA 444–455 1.000 45.7
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAAAGTTTGAGAGTAAGCA 447–458 1.000 45.6
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACAAAAAGTTTGAGAGTAAGCA 448–459 1.000 45.6
psbK-psbI_p4 psbK-psbI TGCCAAATTACCCGAAGCTT ACAAAAAGTTTGAGAGTAAGCA 535–546 1.000 44.7
psbK-psbI_p5 psbK-psbI TTGCCAAATTACCCGAAGCT ACAAAAAGTTTGAGAGTAAGCA 536–547 1.000 44.7
LK95_t006-psbD_p1 LK95_t006-psbD ATTAGCAATCCGCCGCTTTA GAGCAATAGGCCAGACCATC 1175–1211 1.000 81.6
LK95_t006-psbD_p2 LK95_t006-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1153–1189 1.000 80.6
LK95_t006-psbD_p3 LK95_t006-psbD ATTAGCAATCCGCCGCTTTA CCCTTCGTAACCAGTCATCC 1137–1173 1.000 80.1
LK95_t006-psbD_p4 LK95_t006-psbD GAGCGGAAAGAGAGGGATTC GAGCAATAGGCCAGACCATC 1226–1262 1.000 80.0
LK95_t006-psbD_p5 LK95_t006-psbD ATTAGCAATCCGCCGCTTTA AGGCCAGACCATCCTACAAA 1168–1204 1.000 79.9
LK95_t012-LK95_t014_p1 LK95_t012-LK95_t014 CCTCAAGGTTATGAGCCTCG CGACTTACGTCTTAGCACGA 1578–2157 1.000 78.6
LK95_t012-LK95_t014_p2 LK95_t012-LK95_t014 CCTCGTGAGCTACCAAACTG CGACTTACGTCTTAGCACGA 1563–2142 1.000 78.2
LK95_t012-LK95_t014_p3 LK95_t012-LK95_t014 CAAGGTTATGAGCCTCGTGA CGACTTACGTCTTAGCACGA 1575–2154 1.000 75.1
LK95_t012-LK95_t014_p4 LK95_t012-LK95_t014 TCAAGGTTATGAGCCTCGTG CGACTTACGTCTTAGCACGA 1576–2155 1.000 75.1
LK95_t012-LK95_t014_p5 LK95_t012-LK95_t014 TATGAGCCTCGTGAGCTACC CGACTTACGTCTTAGCACGA 1569–2148 1.000 75.0
LK95_t020-psbM_p1 LK95_t020-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 923–926 1.000 59.6
LK95_t020-psbM_p2 LK95_t020-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 924–927 1.000 55.4
LK95_t020-psbM_p3 LK95_t020-psbM CGCGGGGATTGTAGTTCAA AGAATGAACAGTGCAGTAGC 937–940 1.000 54.3
LK95_t020-psbM_p4 LK95_t020-psbM TTCAATTGGTCAGAGCACCG AGGAACTAGAATGAACAGTGCA 930–933 0.923 53.2
LK95_t020-psbM_p5 LK95_t020-psbM TTCAATTGGTCAGAGCACCG GGAACTAGAATGAACAGTGCAG 929–932 0.923 50.7
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT AGTATGGGGAAGGAGTGGAC 731–753 1.000 69.6
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTATGGGGAAGGAGTGGACT 730–752 1.000 69.6
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 789–811 1.000 69.2
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTCT TATGGGGAAGGAGTGGACTC 729–751 1.000 69.2
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT GGGGAAGGAGTGGACTCTAG 726–748 1.000 68.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Aegilops bicornis NC_024831.1 136861 View on NCBI ↗
Aegilops comosa NC_046697.1 136247 View on NCBI ↗
Aegilops cylindrica NC_023096.1 113490 View on NCBI ↗
Aegilops kotschyi NC_024832.1 136868 View on NCBI ↗
Aegilops longissima NC_024830.1 136875 View on NCBI ↗
Aegilops searsii NC_024815.1 136863 View on NCBI ↗
Aegilops sharonensis NC_024816.1 136867 View on NCBI ↗
Aegilops speltoides NC_022135.1 113536 View on NCBI ↗
Aegilops speltoides var. aucheri PQ632087.1 135668 View on NCBI ↗
Aegilops speltoides var. ligustica KJ614404.1 135660 View on NCBI ↗
Aegilops speltoides var. speltoides KJ614406.1 135652 View on NCBI ↗
Aegilops tauschii NC_022133.1 114112 View on NCBI ↗
Aegilops umbellulata NC_046696.1 136743 View on NCBI ↗