Markers + reference

Leymus

13 species · Poaceae · Poales

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Species 13
Genome length 135–137 kb
Candidate markers 266
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 566 0.0154 1.00 48.7 yes View details
trnG-GCC-trnM-CAU LSC 448 0.0193 0.98 53.5 yes View details
trnS-CGA-trnT-GGU LSC 1118 0.0147 0.99 59.5 yes View details
trnT-UGU-trnL-UAA LSC 615 0.0429 0.97 84.4 yes View details
trnF-GAA-ndhJ LSC 581 0.0191 0.91 54.4 yes View details
rbcL-psaI LSC 1642 0.0164 0.97 53.2 yes View details
ycf4-cemA LSC 469 0.0248 0.91 58.0 yes View details
rpl32-trnL-UAG SSC 702 0.0172 0.92 52.1 yes View details
rps19-psbA LSC 136 0.0298 0.97 74.6 no View details
rpl22-rps19 IRb 78 0.0438 1.00 68.4 yes View details
petG-trnW-CCA LSC 121 0.0307 0.95 63.5 yes View details
trnC-GCA-rpoB LSC 1158 0.0093 1.00 55.9 yes View details
trnY-GUA-trnD-GUC LSC 359 0.0142 0.97 55.8 yes View details
trnT-GGU-trnE-UUC LSC 529 0.0095 0.99 54.3 yes View details
ycf3-trnS-GGA LSC 615 0.0084 1.00 54.1 yes View details
trnS-GCU-psbD LSC 980 0.0103 0.98 53.8 yes View details
ndhF-rpl32 SSC 915 0.0106 0.98 53.8 yes View details
infA-rps8 LSC 80 0.0189 1.00 53.0 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AGAAAAAGAAAGAACTTTGAGT 635–650 1.000 43.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AGAAAAAGAAAGAACTTTGAGTT 635–650 1.000 43.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA AGAAAAAGAAAGAACTTTGAGT 633–648 1.000 43.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AAGAAAAAGAAAGAACTTTGAGT 636–651 1.000 43.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA AGAAAAAGAAAGAACTTTGAGT 636–651 1.000 43.8
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TCTACCAAGGGCTATAGTCA 1036–1090 1.000 54.6
trnS-GCU-psbD_p2 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC TCTACCAAGGGCTATAGTCA 1087–1141 1.000 53.0
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TCTACCAAGGGCTATAGTCAT 1036–1090 1.000 51.8
trnS-GCU-psbD_p4 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT TCTACCAAGGGCTATAGTCA 1022–1076 1.000 51.7
trnS-GCU-psbD_p5 trnS-GCU-psbD AGTCCACTCAGCCATCTCTC TCTACCAAGGGCTATAGTCA 1017–1071 1.000 50.9
trnG-GCC-trnM-CAU_p1 trnG-GCC-trnM-CAU GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 563–566 1.000 82.3
trnG-GCC-trnM-CAU_p2 trnG-GCC-trnM-CAU GCGAGCGTAGTTCAATGGTA CAGTTTGGTAGCTCACGAGG 578–581 1.000 81.8
trnG-GCC-trnM-CAU_p3 trnG-GCC-trnM-CAU TAGCGAGCGTAGTTCAATGG CGAGGCTCATAACCTTGAGG 565–568 1.000 81.3
trnG-GCC-trnM-CAU_p4 trnG-GCC-trnM-CAU GCGAGCGTAGTTCAATGGTA GAGCGGAGTAGAGCAGTTTG 591–594 1.000 81.0
trnG-GCC-trnM-CAU_p5 trnG-GCC-trnM-CAU TAGCGAGCGTAGTTCAATGG CAGTTTGGTAGCTCACGAGG 580–583 1.000 80.8
trnS-CGA-trnT-GGU_p1 trnS-CGA-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1129–1320 1.000 47.8
trnS-CGA-trnT-GGU_p2 trnS-CGA-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1125–1316 1.000 47.0
trnS-CGA-trnT-GGU_p3 trnS-CGA-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1126–1317 1.000 47.0
trnS-CGA-trnT-GGU_p4 trnS-CGA-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1131–1322 1.000 47.0
trnS-CGA-trnT-GGU_p5 trnS-CGA-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTAGCACGAG 1189–1380 1.000 46.9
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 612–655 1.000 73.3
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 591–634 1.000 73.3
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 575–618 1.000 73.3
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 554–597 1.000 73.2
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 580–623 1.000 72.5
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 477–487 1.000 80.5
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 444–454 1.000 78.4
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 443–453 1.000 78.2
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 476–486 1.000 76.4
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC GATGCCCGAGTGGTTAATGG CGGTGCTCTGACCAATTGAA 462–472 1.000 75.5

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
Leymus angustus NC_068583.1 135098 View on NCBI ↗
Leymus arenarius NC_063960.1 136715 View on NCBI ↗
Leymus chinensis NC_044900.1 136783 View on NCBI ↗
Leymus cinereus NC_068544.1 136035 View on NCBI ↗
Leymus condensatus NC_068543.1 135057 View on NCBI ↗
Leymus coreanus NC_068542.1 136905 View on NCBI ↗
Leymus duthiei NC_058748.1 136869 View on NCBI ↗
Leymus karelinii NC_068584.1 136727 View on NCBI ↗
Leymus multicaulis NC_058746.1 136437 View on NCBI ↗
Leymus racemosus NC_058747.1 136273 View on NCBI ↗
Leymus racemosus subsp. sabulosus MW628904.1 136756 View on NCBI ↗
Leymus ramosus NC_068585.1 136788 View on NCBI ↗
Leymus secalinus NC_068586.1 136763 View on NCBI ↗