Markers + reference

Triticum

23 species · Poaceae · Poales

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Species 23
Genome length 134–137 kb
Candidate markers 267
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK LSC 232 0.0152 0.97 58.4 yes View details
rps16-trnQ LSC 1061 0.0172 0.68 55.8 yes View details
trnS-psbD LSC 999 0.0063 0.97 57.0 yes View details
trnI-trnL IRb 1497 0.0237 0.91 58.0 yes View details
trnL-trnI IRa 1497 0.0234 0.91 57.4 yes View details
psbT-psbN LSC 48 0.0242 1.00 57.1 yes View details
matK-trnK LSC 598 0.0069 0.97 54.0 yes View details
petA-psbJ LSC 820 0.0034 1.00 51.5 yes View details
ndhB-trnL IRa 603 0.0038 0.92 50.6 yes View details
trnL-ndhB IRb 603 0.0036 0.92 50.1 yes View details
rps19-psbA LSC 140 0.0127 1.00 50.0 no View details
rpl32-trnL SSC 689 0.0060 1.00 47.8 yes View details
psbI-trnS LSC 113 0.0054 1.00 47.3 yes View details
rpl23 LSC 1284 0.0024 1.00 46.9 yes View details
rpl23 IRb 282 0.0025 1.00 40.0 no View details
rpl23 IRa 282 0.0022 1.00 38.6 no 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK_p1 psbA-trnK GCTTGTACTTTCGCGTCTCT AAATGCAAGCACGATTTGGG 365–369 1.000 86.3
psbA-trnK_p2 psbA-trnK AAAACACCGAACCATCCGAT AAATGCAAGCACGATTTGGG 436–440 1.000 85.7
psbA-trnK_p3 psbA-trnK CACCGAACCATCCGATGTAA AAATGCAAGCACGATTTGGG 432–436 1.000 84.9
psbA-trnK_p4 psbA-trnK AAAACACCGAACCATCCGAT CACGATTTGGGGAGAGGTTT 431 0.043 38.6
psbA-trnK_p5 psbA-trnK GCTTGTACTTTCGCGTCTCT CACGATTTGGGGAGAGGTTT 360 0.043 37.7
trnK_p1 trnK TCAAAACTCAGATTGCTCCT AATGTTTTGACAGAAGCGCG 2670 0.043 14.0
trnK_p2 trnK ACTCAGATTGCTCCTTTCTAGT AATGTTTTGACAGAAGCGCG 2665 0.043 13.9
trnK_p3 trnK AGATTGCTCCTTTCTAGTTTCCA AATGTTTTGACAGAAGCGCG 2661 0.043 13.4
trnK_p4 trnK TCAAAACTCAGATTGCTCCTT AATGTTTTGACAGAAGCGCG 2670 0.043 12.8
trnK_p5 trnK TCAAAACTCAGATTGCTCCTTTC AATGTTTTGACAGAAGCGCG 2670 0.043 11.9
matK-trnK_p1 matK-trnK CCATAATCAGGGGCAAATGC CCACGACTGATCCTCAAAGG 726 0.043 35.0
matK-trnK_p2 matK-trnK CCATAATCAGGGGCAAATGC AAGACCACGACTGATCCTCA 730 0.043 34.5
matK-trnK_p3 matK-trnK CCATAATCAGGGGCAAATGC AGACCACGACTGATCCTCAA 729 0.043 34.5
matK-trnK_p4 matK-trnK CCATAATCAGGGGCAAATGC AGAAGACCACGACTGATCCT 732 0.043 33.3
matK-trnK_p5 matK-trnK CCATAATCAGGGGCAAATGC GAAGACCACGACTGATCCTC 731 0.043 30.6
rps16-trnQ_p1 rps16-trnQ CCACAATCGATCGTGTCCTT GAGGTTCGAATCCTTCCGTC 626–1156 1.000 91.3
rps16-trnQ_p2 rps16-trnQ CCACAATCGATCGTGTCCTT AGTGTCGCATAAAACCCGAA 695–1225 1.000 90.5
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 605–1135 1.000 90.3
rps16-trnQ_p4 rps16-trnQ CCACAATCGATCGTGTCCTT CTCGGAGGTTCGAATCCTTC 630–1160 1.000 90.2
rps16-trnQ_p5 rps16-trnQ ATCCACAATCGATCGTGTCC GAGGTTCGAATCCTTCCGTC 628–1158 1.000 89.6
psbI-trnS_p1 psbI-trnS TCTAATGACCCAGGACGGAA TAAAGCGGCGGATTGCTAAT 215–220 1.000 80.7
psbI-trnS_p2 psbI-trnS TCTAATGACCCAGGACGGAA GCTTTGGAACGTGGAGAGAT 247–252 1.000 79.8
psbI-trnS_p3 psbI-trnS TCTAATGACCCAGGACGGAA ATCACGGAAACCTTTCGCTT 263–268 1.000 79.6
psbI-trnS_p4 psbI-trnS ATCTAATGACCCAGGACGGA TAAAGCGGCGGATTGCTAAT 216–221 1.000 78.8
psbI-trnS_p5 psbI-trnS TCTAATGACCCAGGACGGAA CACGGAAACCTTTCGCTTTG 261–266 1.000 78.5
trnS-psbD_p1 trnS-psbD ATTAGCAATCCGCCGCTTTA GAGCAATAGGCCAGACCATC 1150–1194 1.000 83.1
trnS-psbD_p2 trnS-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1128–1172 1.000 82.1
trnS-psbD_p3 trnS-psbD ATTAGCAATCCGCCGCTTTA CCCTTCGTAACCAGTCATCC 1112–1156 1.000 81.6
trnS-psbD_p4 trnS-psbD GAGCGGAAAGAGAGGGATTC GAGCAATAGGCCAGACCATC 1201–1245 1.000 81.3
trnS-psbD_p5 trnS-psbD ATTAGCAATCCGCCGCTTTA AGGCCAGACCATCCTACAAA 1143–1187 1.000 81.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Triticum aestivum NC_002762.1 134545 View on NCBI ↗
Triticum aestivum subsp. sphaerococcum MZ230675.1 134531 View on NCBI ↗
Triticum aestivum subsp. tibeticum KX631429.1 135897 View on NCBI ↗
Triticum aestivum var. vavilovii PQ632091.1 135897 View on NCBI ↗
Triticum carthlicum PQ632093.1 135898 View on NCBI ↗
Triticum carthlicum var. fuliginosum LC375535.1 135897 View on NCBI ↗
Triticum carthlicum var. rubiginosum LC376795.1 135898 View on NCBI ↗
Triticum compactum LC623764.1 135897 View on NCBI ↗
Triticum ispahanicum PV185782.1 135897 View on NCBI ↗
Triticum macha var. colchicum LC375536.1 135899 View on NCBI ↗
Triticum macha var. megrelicum LC372826.1 135899 View on NCBI ↗
Triticum monococcum subsp. aegilopoides PP067985.1 136889 View on NCBI ↗
Triticum monococcum subsp. sinskajae NC_085288.1 136885 View on NCBI ↗
Triticum petropavlovskyi PV185783.1 135898 View on NCBI ↗
Triticum polonicum PQ632094.1 135899 View on NCBI ↗
Triticum timopheevii NC_024764.1 136157 View on NCBI ↗
Triticum timopheevii subsp. araraticum LC655300.1 136118 View on NCBI ↗
Triticum timopheevii subsp. timopheevii PQ625804.1 135899 View on NCBI ↗
Triticum turgidum NC_024814.1 135835 View on NCBI ↗
Triticum turgidum subsp. durum MZ230674.1 134015 View on NCBI ↗
Triticum turgidum subsp. georgicum PQ723554.1 135898 View on NCBI ↗
Triticum turgidum subsp. turanicum PQ632090.1 135899 View on NCBI ↗
Triticum zhukovskyi NC_046698.1 136028 View on NCBI ↗